It’s commonly thought that John the son of Zebedee was the author of the Gospel of John, the figure spoken of in that Gospel as “the disciple whom Jesus loved.” The two are never explicitly identified, however, and there are reasons for questioning this identification.
Here are eight points to consider:
1. John Zebedee is usually listed third among the inner circle of the twelve disciples, after Peter and James.* The Beloved Disciple, however, was ahead of Peter (and presumably the twelve).
* Matt 17:1; Mark 5:37, 9:2, 13:3; Luke 9:28 (and possibly 8:51) has “Peter, John, and James,” though Luke, as Matthew and Mark, always places James before John when mentioning the Zebedee brothers alone.
2. The Beloved Disciple took Mary to his house from the cross “the same hour” (John 19:26-27). John Zebedee lived in Galilee, not Jerusalem.
3. The Beloved Disciple is usually identified as the disciple that was known to the high priest and had access to his palace (John 18: 15); John Zebedee, however, was a Galilean fisherman and was unlikely to have known the high priest and to have been afforded instant entrance to the palace grounds (e.g. see here).
Furthermore, when Peter and John were brought before the Sanhedrin, the members (presumably including the high priest) clearly didn’t have prior acquaintance with them (Acts 4:5-6, 13).
4. Jesus predicated that the Zebedee brothers, James and John, would drink the same cup Jesus had to drink, and be baptized with the same baptism he would have to undergo (Matthew 22: 22-23; Mark 10:38-39; cf. my summary of the evidence for John Zebedee’s martyrdom). The Beloved Disciple (John the Evangelist) is held to have died naturally.
5. The Gospel of John says little about Galilee and mostly recounts events in Jerusalem. Perhaps the disciple was a Jerusalemite. Not a single episode in which only the inner circle of Peter, James and John were present is recorded in the Fourth Gospel.
6. The disciples all forsook Jesus and fled. The Beloved Disciple stayed with him at the cross.
7. The Beloved Disciple was serene and contemplative; the son of Zebedee was rash and impulsive.
8. The Beloved Disciple is an anonymous figure in the Gospel of John, and this anonymity is maintained throughout the account. There is a reference to the “Zebedee brothers” (John 21:2), however, suggesting that he was not one of them.