A: The phrase “the disciple whom Jesus loved” is mentioned only in the Gospel of John, and in 5 places within that Gospel: (Jn 13:23)(Jn 19:26)(Jn 20:2)(Jn 21:7,20).

     We can clearly see that “the disciple whom Jesus loved” wrote this Gospel from (Jn 21:20-24). However, since the author of the Gospel of John does not clearly name himself, there have been some over time who have questioned who the author is. Nevertheless, nearly all scholars agree that the disciple John is the author. Therefore, “the disciple whom Jesus loved” would be referring to John.

     That John wrote this book, and is in fact “the disciple whom Jesus loved,” has overwhelming proofs. The early church, and the early church fathers (i.e. Papias, Polycarp, Justin Martyr, Irenaeus) were totally united in the belief that John wrote this Gospel (which is why it was named “The Gospel Of John”).  In fact, it is interesting to note that Irenaeus was a pupil of Polycarp (69 A.D-155 A.D.)(who was martyred app. 155 A.D. after being a Christian for 86 years), and Polycarp was a pupil of John. Therefore, there was only one link between Irenaeus and John. In his book, “Against Heresies,” Irenaeus called John, “the disciple of the Lord, who had leaned upon his breast.”

     There is also evidence within the book that John wrote it. For example, as we said above, “the disciple whom Jesus loved” wrote the book (Jn 21:20-24). We know from earlier in Chapter 21 that this disciple had to be one of 7 people: Peter, Thomas, Nathanael, the sons of Zebedee (James and John: Mt 4:21), or one of two other unnamed disciples (See: Jn 21:2).  Peter didn’t write it because the “disciple whom Jesus loved” spoke to Peter (Jn 21:7). Peter also asked Jesus a question about “the disciple whom Jesus loved” in (Jn 21:20-23).  In Jesus’ response to Peter’s question, He seemed to indicate that “the disciple whom Jesus loved” would not die a martyr’s death (although the text says Jesus did not specifically say that). Historical evidence clearly shows us that John lived until app. 98 A.D., and died a natural death (go here for more on this). John was the only apostle who was not martyred. James died shortly after Jesus said these words, being the first apostle to be martyred (Acts 12:2), so it seems very unlikely he was “the disciple whom Jesus loved.”

     Peter, James, and John were a part of Jesus’ “inner circle.” Jesus allowed them to witness things that none of the other disciples were allowed to witness. For example:
The daughter of Jarius being raised from the dead: (Mk 5:35-43)(Lk 8:49-56)
The Transfiguration: (Mt 17:1-9)(Mk 9:1-10)(Lk 9:27-36)
Jesus’ agony in Gethsemane: (Mt 26:36-46)(Mk 14:32-42)

     This being said, it seems unlikely that any of the other 4 disciples remaining from (Jn 21:20-24)(not counting John): Thomas, Nathanael, or the 2 unnamed disciples (keeping in mind Matthew had already written one Gospel, and it wasn’t Judas Iscariot) could have written this book given its significance.

     One other thing that points to John as the author of John is that it shares some important similarities with the book of Revelation, which we KNOW that John wrote (Rev 1:1,4,9)(Rev 22:8). For example:

Jesus is called “the Word” (Rev 19:13)(Jn 1:1,14). Other than (1 Jn 1:1, 5:7), this is used nowhere else in the Bible.
Jesus is called a “Lamb” (26 times in Rev) (Jn 1:29,36). He is called a “Lamb” nowhere else in the Bible.
Only in (Rev 21:6)(Rev 22:17)(Jn 4:10-11)(Jn 7:38) is Jesus described as living “water.”
Only in (Rev 1:7)(Jn 19:37) is the Greek word “ekkenteo” used for the word “pierced.”
The word “true” is used 20 times in the Gospel of John and 10 times in Revelation. This is by far the most of any other books in the Bible.

(Revelation also shares with John’s other writings the contrasts of light and darkness, good vs. evil, love vs. hatred, etc…)

     Putting these things together, it seems conclusive that the disciple John was the author of The Gospel of John, as well as “the disciple whom Jesus loved.” I also find it interesting that by almost all accounts, John is considered to have been the youngest disciple, and perhaps was even a teenager when called by Jesus. I have made note of the fact that many times in the Old Testament, God chose to work through the youngest rather than the oldest (against the customs of the time). This also seems to be the case with John.

     Finally, let me address the problem that some have over John saying he WAS “the disciple whom Jesus loved.” By saying this, some believe it makes John sound like he was saying he was Jesus’ “favorite,” and that Jesus loved him “more” than the other disciples. The fact that John had a “special” relationship with Jesus seems clear, since he was in Jesus’ “inner circle.” Jesus also singled John out for several important tasks such as caring for His mother after He died (Jn 19:25-27), and directly giving him the book of Revelation to write.  However, I don’t believe John was saying he was Jesus’ “favorite,” or that Jesus “loved him more.” Most scholars believe that when John said he was “the disciple whom Jesus loved,” it was more out of humility than pride. He did not want the focus to be on his name (John), but instead on the love Jesus had for him. He was amazed by this great love, and wanted to stress it.

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