"A Prayer for Owen Meany" is told from the viewpoint of John Wheelright. Owen Meany is a Christ-like figure from birth. His parents believe he was a virgin birth. Owen dies as a martyr, believing, like Jesus, that he is fulfilling God's purpose. The purpose of portraying Owen as a Christ-like figure is to show the battle between faith and doubt in all religions. John cannot believe in God without proof of his existence. Owen's faith is strong, and he challenges and ultimately resolves John's doubts.

Owen is John's best friend and accidentally kills John's mother with a baseball. John struggles with grief after his mother dies. He does not see her death through the lens of religion. Owen can cope better with the death by framing it as God's will:

GOD HAS TAKEN YOUR MOTHER. MY HANDS WERE THE INSTRUMENT. I AM GOD'S INSTRUMENT.

John forgives Owen, and the boys remain friends throughout the rest of Owen's life. John begins to see Owen as an exceptional person who stands apart from other people. John is ambivalent about religion, but he has strong faith in Owen, who often rebukes him for his lack of faith in God.

Owen dies as a martyr, saving the lives of ten children. He predicted the exact date of his death and wrote about it in his journal, much like Jesus prophesied his own death. He also made preparations for his death such as carving his own gravestone.

Owen's prophecies regarding his death and the manner of his death awaken spirituality in John, who becomes a Christian. John sees Owen's death as proof of God's existence which resolves his doubts about God. John spends the rest of his life talking and writing about Owen and his life. He becomes a disciple, much like the prophet John becomes the first disciple of Jesus. He prays for Owen to return, much like Christians hope for the return of Christ.