What does John 1:49 mean?

Jewish people used the term Rabbi to refer to religious leaders and scholars. It literally means "honorable sir," or even "master." John frequently explains Hebrew words and culture for his readers (John 9:7; 20:16). John had already defined the term "Rabbi" as "Teacher" (John 1:38).

It's almost certain the conversation between Jesus and Nathanael was longer than the summary recorded in the gospel of John. However, the change in Nathanael's attitude is dramatic. Within a few moments, he goes from insulting Jesus' hometown, to doubting His knowledge, to referring to Him as Rabbi. Calling Jesus the "Son of God" refers to prophecies of the Messiah (Daniel 9:25). The Promised One is described as the Son of God in Psalm 2.

Nathanael also uses the sixth of the seven names for Jesus in chapter 1: "the King of Israel." Isaiah 11:1–2 describes the future King as having God's spirit of wisdom. When Nathanael doubted that Jesus would be worth knowing, Philip suggested meeting Him (John 1:46). That made all the difference.

This verse is also the second of seven "witnesses" in the gospel of John. These are people who explicitly state that Jesus is the Christ: the Messiah, the Son of God. The others include John the Baptist (John 1:29), Peter (John 6:69), the blind man (John 9:35–38), Martha (John 11:27), Thomas (John 20:28), and Jesus Himself (John 5:25; John 10:36).