Before I explain, it is important to remember that none of our prayers are perfect. We stutter, stammer, pray selfishly, pray without heart, and sometimes pray with quite a bit of doubt. Thankfully we have a loving Father in heaven who hears us despite our imperfections, we have the Holy Spirit interceding within us (Rom. 8:26) and we have Christ interceding for us before the Father (Rom. 8:34). Because of these realities, when we pray with true faith, albeit imperfect and weak faith, God hears our prayers.
The basic biblical way to think about prayer is this: We pray to the Father, through the Son, because the Spirit is at work in us (Luke 11:2, Rom. 8:26, Rom. 8:34, etc.). If we’re praying to the Father, we do so in the name of Christ, not in the name of the Father (John 16:24, 26). And if we’re praying to Jesus (like Stephen did in Acts 7:59) we don’t pray to him in his name; that would be redundant. Based on this biblical logic, I’d argue we shouldn’t end our prayers with, “in Your name, Amen.” Instead, we should ordinarily end them with “In Jesus’ name, Amen,” or “In Christ’s name, Amen” (or something similar).
A good question comes up: “What does it mean to pray in Jesus’ name?” The Westminster Larger Catechism has a helpful answer:
“To pray in the name of Christ is, in obedience to his command, and in confidence on his promises, to ask mercy for his sake, not by bare mentioning of his name, but by drawing our encouragement to pray, and our boldness, strength, and hope of acceptance in prayer, from Christ and his mediation” (cf. John 14:13-14, John 16:24, Dan. 9:17, Matt. 7:21, Heb 4:14-16). [Q/A 180]
The Catechism goes on to explain that we must pray only in Christ’s name because he’s the only mediator between God and man (John 14:6, Eph. 3:12, etc.). Here’s how A. W. Pink stated it in his Exposition of the Gospel of John (commenting on John 14:14):
What is meant by asking in the name of Christ? Certainly it is much more than the mere putting of His name at the end of our prayers, or simply saying, “Hear me for Jesus’ sake.” First, it means that we pray in His person, that is, as standing in His place, as fully identified with Him, asking by virtue of our very union with Himself. When we truly ask in the name of Christ, He is the real petitioner. Second, it means, therefore, that we plead before God the merits of His blessed Son. When men use another’s name as the authority of their approach or the ground of their appeal, the one of whom the request is made looks beyond him who presented the petition to the one for whose sake he grants the request. So, in all reverence we may say, when we truly ask in the name of Christ, the Father looks past us, and sees the Son as the real suppliant. Third, it means that we pray only for that which is according to His perfections and what will be for His glory. When we do anything in another’s name, it is for him we do it. When we take possession of a property in the name of some society, it is not for any private advantage, but for the society’s good. When an officer collects taxes in the name of the government, it is not in order to fill his own pockets. Yet how constantly do we overlook this principle as an obvious condition of acceptable prayer! To pray in Christ’s name is to seek what He seeks, to promote what He has at heart!
We shouldn’t be so obsessed with the exact wording of our prayer that we just give up and stop praying! Again, our heavenly Father loves us as his children in Christ. Christ intercedes for us before the Father. Furthermore, the Spirit of God is at work in us, helping us to pray when we can’t find the words. Our heavenly Father hears our prayers because of Christ, not because we use the perfect words. In that light, we pray “in Jesus’ name, Amen!”