Prayer (John 9:31) | Shaun Doyle

Happy Father’s Day to earthy fathers, and praise to God as He is our one true Father who is in Heaven (Mat 23:9). As children of God, we should have an eagerness to communicate with our Father through prayer.

I admit I need help with my prayer life. I find myself saying similar prayers and making them mostly at meals, or too often mainly praying for myself and immediate family. I started to become more convicted about prayer, building up questions that needed to be answered.

What exactly is prayer? How do we pray? Since God is sovereign and knows all that we need before we ask, why do we need to pray? Do our prayers affect the ultimate purposes and will of God? When does God listen or not listen to our prayers? As we struggle to understand how to pray, remember that even the disciples, asking Jesus to teach them how to pray in Luke 11.

What is prayer?

  • Prayer is the way in which we communicate to God.
  • The Westminster Shorter Catechism 98 describes this as “ an offering up of our desires unto God, for things agreeable to His will, in the name of Christ, with confession of our sins, and thankful acknowledgment of His mercies”
  • The 1689 Baptist Confession of Faith says that “Prayer, with thanksgiving, is to be made in the name of the Son, by the help of the Spirit, according to His will; it is done with understanding, reverence, humility, fervency, faith, love, and perseverance”
  • RC Sproul with Ligonier Ministries says “The first element of prayer should be adoration, or praise. The Psalms, which are inspired samples of godly prayer, are heavily weighted on the side of adoration. Second, prayer should include confession of our sin; as we remember who we are when we come into God’s presence, we see that we have come short of His holiness and have need of His forgiveness. Third, when we pray, we should always give thanks, remembering the grace and mercy God has shown toward us. Fourth, prayer rightly includes supplication or petition, bringing our requests for the needs of others and ourselves to God.

Prayer is not a mystical exercise in which we sit in silence, waiting for God to speak to us in a still small voice, nor should we automatically contribute our emotions as the voice of God. The Lord does indeed speak to us, through the inerrant, authoritative, and living written Word of God.

Why do we pray?

  • The very reason we pray is because of God’s sovereignty, for He is omniscient, omnipresent, and omnipotent. because He is able to do exceedingly abundantly beyond ALL that we ask or think. because He is the Alpha and Omega,
  • We should be praying first and foremost to the advance the kingdom of God in our lives, in the church, and in the world.
  • We can also be assured that God knows what is best for His people and that He is working for our good and His glory, whether He says yes or no to our supplications, whether He allows us to endure trials and persecution or not.
  • We are to conform to the image of Christ, and as He prayed, so should we. No man ever prayed more fiercely or more effectively. We see Christ offered prayers to the Father, going up a mountain to pray by Himself (Mat 14:23, Luk 6:12), praying in Gethsemane when He was distressed and troubled (Mar 14:32), modeling how prayer ought to be done (Mat 6:6-13), giving thanks that He has been heard by God (Joh 11:41), breaking bread with His disciples and giving thanks to God, even driving out robbers to ensure His house was a house of prayer (Luk 19:46)

Do our prayers affect the ultimate purposes and will of God?

  • The Bible says there are certain things God has decreed from all eternity.
  • Those things will inevitably come to pass, for even though Jesus prayed for the Father to take the cup [of wrath] from Him (Luk 22:42), this prayer was denied.
  • Our prayers can not change what God has purposed to accomplish.
  • However, James 5:16 says “The prayer of a righteous person has great power as it is working” thus our prayers do affect some circumstances, as long as it still falls under the ultimate will of God.
  • One prayer that altered circumstances can be found in James 5:17-18: “Elijah was a man with a nature like ours, and he prayed fervently that it might not rain, and for three years and six months it did not rain on the earth. Then he prayed again, and heaven gave rain, and the earth bore its fruit.”

How has God instructed us to pray?

OPEN TO PSALM 51. This is an inspiring prayer that we should all emulate.

  • See how David prayed after he committed adultery with Bathsheba and killed her husband.
  • He prayed to the Lord for mercy and deliverance.
  • He recognized that it is indeed the Lord who cleanses and regenerates the heart, that we are incapable of making ourselves alive from our spiritual death as explained in Ephesians 2.
  • He understood that such sin is truly evil in the sight of a holy and just God.
  • He confirms that none are good, even from birth, despite various religious beliefs that infants are born holy and innocent.
  • Even after all that sin, God heard his prayer because he came to God with a humble and repentant heart. For in 1 John 1:9, The Lord says that “If we confess our sins, he is faithful and just to forgive us”


  • In both Luke 11 and Matthew 6, Jesus models how we ought to pray. “One of his disciples said to him, “Lord, teach us to pray, as John taught his disciples.”
  • In these verses, they describe the holiness and sovereignty of God; our thankfulness and dependence on God; the need to be forgiven and forgive; strength to withstand temptation by putting on the armor of God and hiding His Word within our heart; and deliverance from evil – salvation through glorification.


  • Many theologians will call this the boldest prayer ever prayed.
  • While many in Scripture bowed their knees as a form of submission, it is not a required posture.
  • Even when Paul was imprisoned and in need, he prayed for his fellow believers that they would be strengthened by the Spirit so that Christ would fully dwell within their hearts,
  • so that they would understand the magnificent love of Christ, which leads to the fullness of God within us.
  • Can you imagine any greater request than to be filled with the fullness of God? With this fullness, there is nothing left of the old self, no more heart of stone. Dale Partridge with Relearn Church said this fullness will bring about obedience, fruitful works, holiness, hope, righteousness, boldness for truth.
  • This prayer should make us realize the overwhelming sensitivity we should have towards the spiritual needs of others.
  • This is why fellowship is so important, even during a pandemic. As Hebrews 10:25 says, do NOT neglect to meet together, as is the habit of some, but encouraging one another, and all the more as you see the Day drawing near.

When we consider prayer, Scripture instructs to

  • Pray only to God our King (Ps 5:2), not to saints, Mary, or idols who can’t save (Is 45:20);
    • In a recent conversation with a professing catholic, she stated  “we pray to Mary, not worship her. It’s like asking a friend in this world to pray for you, except we know she’s right there next to Jesus to intercede for us”
    • We are only to pray to God, prayer to anything else is idolatry. Beware of such church traditions. Jesus addresses this similarly in Matthew 15:3, “why do you break the commandments of God for the sake of your traditions?” Mary has no authority or power, she is not our mediator, intercessor, or high priest. She is not omnipotent, omniscient, or omnipresent, and merely was made in the image of God like you and I.
  • Pray only for the living, not the dead. As the 1689 Baptist confession of faith describes, Prayer is to be made for things lawful, and for all sorts of men living, or that shall live hereafter; but not for the dead (1 Timothy 2:1, 2; 2 Samuel 7:29; 2 Samuel 12:21-23; 1 John 5:16 ). Why do people say to pray for someone who just died? This places an uncomfortable and unrealistic expectation on one who most likely is emotionally struggling. There is no purgatory, for people instantly meet the judgment seat of God. Hebrews 9:27 says “just as it is appointed for man to die once, and after that comes judgment.”
    • Giving of alms and prayers to loose the sins of the dead in purgatory stems from the Apocrypha, which you can find today in Catholic Bibles. These are a collection of 13 books that are external to the accepted Biblical canon. These were written during the 400 year time span between the last of the Old Testament books, Malachi, and the first reference to John the Baptist in the NT book of Matthew.
    • The Protestant Reformation had drastic religious changes (years 1517 to 1648), and major reformers like Martin Luther, John Calvin and Henry VIII challenged the Catholic Church’s authority and ability to define Christian practice. After this reformation, many Protestant Bibles began to exclude the apocrypha, since these were not divinely inspired and profoundly heretical
    • It’s also worthwhile to know that none of the New Testament prophets and disciples ever quoted or referred to these books.
    • 2 Maccabees 12:45–46 says “it is therefore a holy and wholesome thought to pray for the dead, that they may be loosed from sins.”
    • Tobit 12:9 says “For alms delivereth from death, and the same is that which purgeth away sins, and maketh to find mercy and life everlasting.”
    • If anyone truly knows Scripture, nothing can cleanse us from our sin except the Lord through repentance and faith. This verse also implies that any acts of ourselves can absolve another’s sin – this is blatantly false. We can not cause others to be saved and forgiven. Ephesians 2:8 rebukes verses like this, clearly stating that “For by grace you have been saved through faith. And this is not your own doing; it is the gift of God.”
  • Cry out for discernment and lift our voice for understanding (Prov 2:3-4);
  • Confess our sins to the Lord (Ezra 10:1, Daniel 9:4, Nehemiah 1:5-7);
  • Pray in a pure manner (Job 16:17);
  • Devote ourselves to prayer (Acts 2:42); continue steadfast in prayer (Col 4:2); Pray without ceasing (1 Thessalonians 5:17)
  • Prayer should include thanks and joy for all circumstances (Luke 18:1, 1 Thes 5:16-18, James 1:2). We have this heart of joy because we know that for those who love God, ALL things work together for good, for those who are called according to His purpose.
  • Prayer should include a submission of ourselves to His will (Mat 26:39); hence, let Your will be done on earth as it is in heaven
  • Pray is both private (Mat 6:6/14:23) and corporate (Acts 1:14/2:42/12:5/14:23);
    • While prayer can be private, it does not mean that it is to be hidden. In Daniel 6, When King Darius issued a decree that no one may pray to any other, what did Daniel do? Verse 10 says “Now when Daniel learned that the decree had been published, he went home to his upstairs room where the windows opened toward Jerusalem. Three times a day he got down on his knees and prayed, giving thanks to his God, just as he had done before.” He knew of this decree yet still prayed openly – could we say the same? He could have easily closed His doors, but he chose not to. He simply had a reverential fear of the Lord more than the fear of man. Matthew 5:14 says “you are the light of the world. A city on a hill cannot be hidden” and similarly in Acts 5, Peter and the apostles replied back to the high priest saying “we MUST obey God rather than men.” We are not to avoid persecution, but as Acts 2:3 says, “Share in suffering as a good soldier of Christ Jesus” since our aim is To please the one who enlisted us.
  • Prayer should not draw attention to ourselves, nor include empty and repetitive phrases as if it influences the Lord to hear our prayer (Mat 6:5-7);
  • Pray in the Holy Spirit (Jud 1:20)
    • What do we do when we are grieved, burdened, overwhelmed, and in a lack of words? We can pray silently, in our hearts. Romans 8:26 says “In the same way, the Spirit helps us in our weakness. We do not know what we ought to pray for, but the Spirit himself intercedes for us through wordless groans.” Similarly, in 1 Samuel 1:13, “Hannah was praying in her heart, and her lips were moving but her voice was not heard.” I find myself giving silent prayers when I am heavily convicted of my sin, when God provides me godly sorrow that leads to repentance.
  • Let our requests be made known to God with thanksgiving (Phil 4:6)


  • In Colossians 1, Paul is writing to the saints and faithful brothers in Christ, saying that he has not ceased to pray for them, asking that they may be filled with the knowledge of His will in all spiritual wisdom and understanding. How often do we pray that our fellow believers may continue to grow in the knowledge and understanding of the Lord? Or are we just assuming they are?
  • Pray for one another for restoration and sanctification (Jam 5:16)
  • Pray for those facing persecution (Acts 12:5);
  • Pray for those who persecute others (Mat 5:44);
  • Pray for those who are suffering (Jam 5:13)
  • Pray that God provides the Spirit of wisdom and knowledge of Him and enlightens the hearts of others (Eph 1:16-18);
  • Pray that others faith may be strengthened (Luke 22:32);
  • Pray for peace, that those who love God may be secure (Ps 122:6);
  • Pray for those in authority. The 1689 says…We ought to make supplications and prayers for kings and all that are in authority, that under them we may live a quiet and peaceable life, in all godliness and honesty. 5 1 Tim. 2:1–2
  • When we tell others we will pray for them, make sure you do! Let our yes be yes as Mat 5:37 points out.

When does God hear our prayers?

  • God attends to our prayer for those who fear Him (Ps 66:19), repent of their sin (Ps 51), and depend on Him for grace and deliverance (Ps 6);
  • God regards the prayer of the upright, righteous, and poor (Prov 15:8, Prov 15:29, 1 Pet 3:12, James 5:16, Ps 102:17);
  • God listens to our prayer when we worship Him and do His will (John 9:31);
  • God provides us with generous amounts of wisdom when we ask in faith (Jam 1:5-7)

When does God ignore our prayers? When does He consider our prayers an abomination?

  • There are many instances when the Lord does not hear our prayers. Proverbs 1:28-29 says, “Then they will call upon me, but I will not answer; they will seek me diligently but will not find me. Because they hated knowledge and did not choose the fear of the Lord”
  • When we habitually practice sin without repentance. Is 59:1-2 says “Behold, the Lord’s hand is not shortened, that it cannot save, or his ear dull, that it cannot hear; but your iniquities have made a separation between you and your God, and your sins have hidden his face from you so that he does not hear.” and similarly, John 9:31 says “We know that God does not listen to sinners, but if anyone is a worshiper of God and does his will, God listens to him.”
    • This sinner does not worship the Lord and obey His Will. Can this verse apply to a genuine Christian? I would say yes, for even Christians stumble and fall into sin. in what ways do we continue to sin, either through ignorance or through intentionality? When we repent, Do we know what sins we are specifically asking forgiveness for? Lord, forgive me for sinning against You, I beg you for mercy, wisdom, understanding, cleanse my heart and my hands, make me new, indwell with the HS and sanctify me more and more into the image of Christ. Our worship is more than verbal praise and music but the daily walk of obedience to the Lord. Read Thomas Watson’s doctrine of repentance.
  • When we forget the Lord our God and go after other gods and serve them and worship them (Deut 8:19).
    • Remember the Lord and continue to Pray even when times are good. The time that we think we need not pray is the most concerning, we can not forget the mercy and love, we can not become desensitized to our sin to where we think we are a good person, to where we need not repent.
  • God does not grant prayers when done with the wrong motives, when geared towards our pleasures (Jam 4:3)
    • Matthew 7:7, “Ask, and it will be given to you; seek, and you will find; knock, and it will be opened to you.
    • And John 14:14, “if you ask me anything in my name, I will do it.”
    • Slapping on the holy name of Jesus to a prayer does not mean it will be answered. What we should understand from this, is that our prayers should be in alignment with the purposes, will, and nature of God, in accordance with His written Word.
  • When we shut our ears to the poor (Prov 21:13)
  • When have hands that are covered in blood (Is 1:15),
  • When we practice evil deeds (Mic 3:2-5);
  • When we have wickedness in our heart (Ps 66:18) – hatred, bitterness, unforgiveness, hardness of heart, a love of sin and hatred of righteousness
  • God can be angry with people’s prayer (Ps 80:4);
  • God considers prayer an abomination when one refuses to listen to the Law (Prov 28:9);
  • God hinders prayers of husbands who do not show understanding and honor to their wives (1 Pet 3:7);


Summary of key points. How do we apply these things? Printed out study summary in the back that you can pick up after service.


Lord, we deserve eternal separation from you for we have sinned against you, change our

heart that we may be broke over and hate all sin, love righteousness, and strive to obey,

trust, and serve You all the days of our life, until you call us home. Blessed be the God and

Father of our Lord Jesus Christ, for In him we have redemption through his blood. Thank

you for loving us, thank you for undeserved mercy poured out on us. You alone are good,

and deserve all the praise.

Scriptural References:

2 Chronicles 6:26, “When heaven is shut up and there is no rain because they have sinned against you, if they PRAY toward this place and confess your name and turn from their sin, when you afflict them, then hear in heaven and forgive the sin of your servants, your people Israel, when you teach them the good way in which they should walk, and grant rain upon your land, which you have given to your people as an inheritance.”

Ezra 10:1, “While Ezra prayed and made confession, weeping and casting himself down before the house of God”

Nehemiah 1:5-7, “And I said, “O Lord God of heaven, the great and awesome God who keeps covenant and steadfast love with those who love him and keep his commandments, 6 let your ear be attentive and your eyes open, to hear the prayer of your servant that I now pray before you day and night for the people of Israel your servants, confessing the sins of the people of Israel, which we have sinned against you”

Job 16:16-17, “My face is red with weeping, and on my eyelids is deep darkness, although there is no violence in my hands, and my prayer is pure.”

Psalm 5:2, “Give attention to the sound of my cry, my King and my God, for to you do I pray.”

Psalm 6 – See Entire Chapter

Psalm 51 – See Entire Chapter

Psalm 61: 1: “Hear my cry, O God, give heed to my prayer”

Psalm 66:16-19 “Come and hear, all you who fear God, and I will tell what he has done for my soul. I cried to him with my mouth, and high praise was on my tongue. If I had cherished iniquity in my heart, the Lord would NOT have listened. But truly God has listened; he has attended to the voice of my prayer.”

Psalm 80:4, “O Lord God, how long will you be angry with your people’s prayers?”

Psalm 102:17, “He regards the prayer of the destitute”

Psalm 122:6, “Pray for the peace of Jerusalem! “May they be secure who love you!”

Psalm 145:19, “He fulfills the desire of those who fear him; he also hears their cry and saves them”

Proverbs 2:1-5, “My son, if you receive my words and treasure up my commandments with you, making your ear attentive to wisdom and inclining your heart to understanding; yes, if you call out for insight and raise your voice for understanding, if you seek it like silver and search for it as for hidden treasures, then you will understand the fear of the Lord and find the knowledge of God.”

Proverbs 1:28-29, “Then they will call upon me, but I will not answer; they will seek me diligently but will not find me. Because they hated knowledge and did not choose the fear of the Lord”

Proverbs 15:8, “The Lord detests the sacrifice of the wicked, but the prayer of the upright pleases him.”

Proverbs 15:29, “The Lord is far from the wicked, but he hears the prayer of the righteous.”

Proverbs 21:13, “Whoever shuts their ears to the cry of the poor will also cry out and not be answered.”

Proverbs 28:9, “He who turns away his ear from listening to the law, even his prayer is an abomination”

Isaiah 1:15, “When you spread out your hands, I will hide my eyes from you; even though you make many prayers, I will not listen;  your hands are full of blood.”

Isaiah 45:20, “Assemble yourselves and come; draw near together, you survivors of the nations!

They have no knowledge who carry about their wooden idols, and keep on praying to a god that cannot save”

Daniel 9:4-5, “I prayed to the Lord my God and made confession, saying, “O Lord, the great and awesome God, who keeps covenant and steadfast love with those who love him and keep his commandments, we have sinned and done wrong and acted wickedly and rebelled”

Micah 3:2-4, “you who hate the good and love the evil…Then they will cry to the Lord, but he will not answer them; he will hide his face from them at that time, because they have made their deeds evil”

Matthew 5:44-45, “But I say to you, Love your enemies and pray for those who persecute you, so that you may be sons of your Father who is in heaven.”

Matthew 6:6-13, “But you, when you pray, go into your room, and when you have shut your door, pray to your Father who is in the secret place; and your Father who sees in secret will reward you openly. And when you pray, do not use vain repetitions as the heathen do. For they think that they will be heard for their many words. “Therefore do not be like them. For your Father knows the things you have need of before you ask Him. In this manner, therefore, pray: Our Father in heaven, Hallowed be Your name. Your kingdom come. Your will be done, On earth as it is in heaven. Give us this day our daily bread. And forgive us our debts, As we forgive our debtors. And do not lead us into temptation,But deliver us from the evil one. For Yours is the kingdom and the power and the glory forever. Amen”

Matthew 14:23, “And after he had dismissed the crowds, he went up on the mountain by himself to pray.”

Mark 14:32, “And they went to a place called Gethsemane. And he said to his disciples, “Sit here while I pray.”

Luke 6:12, “In these days he went out to the mountain to pray, and all night he continued in prayer to God.”

Luke 18:1, “And he told them a parable to the effect that they ought always to pray and not lose heart.”

Luke 19:46, “It is written, ‘My house shall be a house of prayer,’ but you have made it a den of robbers.”

Luke 22:32, “I have prayed for you that your faith may not fail.”

Luke 22:41-42, “And he withdrew from them about a stone’s throw, and knelt down and prayed, saying, “Father, if you are willing, remove this cup from me. Nevertheless, not my will, but yours, be done.”

John 9:31, “We know that God does not listen to sinners, but If anyone is a worshiper of God and does his will, God listens to him.”

John 11:41, “So they took away the stone. And Jesus lifted up his eyes and said, “Father, I thank you that you have heard me.”

Acts 1:14, “All these with one accord were devoting themselves to prayer, together with the women and Mary the mother of Jesus, and his brothers.”

Acts 2:42, “And they devoted themselves to the apostles’ teaching and the fellowship, to the breaking of bread and the prayers”

Acts 12:5, “So Peter was kept in prison, but earnest prayer for him was made to God by the church.”

Acts 14:23, “​​And when they had appointed elders for them in every church, with prayer and fasting they committed them to the Lord in whom they had believed.”

Romans 8:28, “And we know that for those who love God all things work together for good, for those who are called according to His purpose.”

1 Corinthians 14:14, “For if I pray in a tongue, my spirit prays but my mind is unfruitful.”

Ephesians 1:16-18, “I do not cease to give thanks for you, remembering you in my prayers, that the God of our Lord Jesus Christ, the Father of glory, may give you the Spirit of wisdom and of revelation in the knowledge of him, having the eyes of your hearts enlightened, that you may know what is the hope to which he has called you”

Philippians 4:6, “do not be anxious about anything, but in everything by prayer and supplication with thanksgiving let your requests be made known to God.”

Colossians 4:2, “Continue steadfastly in prayer, being watchful in it with thanksgiving.”

1 Thessalonians 5:16-18, “Rejoice always, pray without ceasing, give thanks in all circumstances; for this is the will of God in Christ Jesus for you”

James 1:5-7, “If any of you lacks wisdom, let him ask God, who gives generously to all without reproach, and it will be given him. But let him ask in faith, with no doubting, for the one who doubts is like a wave of the sea that is driven and tossed by the wind. For that person must not suppose that he will receive anything from the Lord”

James 4:3, “You ask and do not receive, because you ask wrongly, to spend it on your passions.”

James 5:16, “The prayer of a righteous person has great power as it is working”

1 Peter 3:7, “Likewise, husbands, live with your wives in an understanding way, showing honor to the woman as the weaker vessel, since they are heirs with you of the grace of life, so that your prayers may not be hindered”

1 Peter 3:12, “For the eyes of the Lord are on the righteous, and his ears are open to their prayer. But the face of the Lord is against those who do evil.”

1 Peter 3:12, “For the eyes of the Lord are on the righteous, and his ears are open to their prayer. But the face of the Lord is against those who do evil.”

1 John 5:15, “And if we know that he hears us in whatever we ask, we know that we have the requests that we have asked of him.”

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