Nathanael was startled that a stranger spoke as if He already knew his heart. Jesus had not just named him; He had described his character: a true Israelite with no guile (John 1:47). Nathanael had come expecting little from a man of Nazareth (John 1:46), so he asked how Jesus could possibly know him. The question is honest surprise, a man trying to understand what had just happened.

Jesus answered plainly: "Before that Philip called thee, when thou wast under the fig tree, I saw thee" (John 1:48). That one sentence was enough. Nathanael answered, "Rabbi, thou art the Son of God; thou art the King of Israel" (John 1:49). Jesus then promised him that he would "see greater things than these" (John 1:50).

The KJV word "Whence" translates the Greek pothen, "from where." Nathanael literally asks, "From where do you know me?" He wanted to know the source of Jesus' knowledge.

The text does not say what Nathanael was doing under the fig tree. Barnes says it is "not improbable" that he went there "for the purpose of meditation and prayer." Gill notes that it was usual for Jewish teachers "to read, and study in the law, under fig trees." Matthew Henry suggests he was "probably" in prayer where "no human eye observed him." These are careful guesses; John leaves the details private.

This exchange shows that Jesus knows people completely. He did not need to be told who Nathanael was. Barnes explains that Jesus did not mean He had been bodily present, but that "he knew his thoughts, his desires, his secret feelings and wishes." Gill calls it an instance of Christ's omniscience. John says the same thing a little later: Jesus "knew what was in man" (John 2:25).

For Nathanael, being fully known was not a threat but the doorway to faith. The One who saw him in private was the Son of God and King of Israel (John 1:49). Jesus' knowledge of us is the knowledge of One who calls and welcomes.