Nathanael couldn't figure out how Jesus knew who he was. They had never met, and Nathanael knew nothing at all about Jesus. Though he had no opinion about Jesus, Jesus had a high opinion of him, saying, "Here is a true Israelite, in whom there is nothing false" (John 1:47). That's high praise coming from Jesus who could spot hypocrisy a mile away. (Since He was the Son of God, distance didn't matter. He knew a hypocrite before he opened his mouth and made it official.)
Evidently Nathanael was a true believer among the ancient Israelites, a man patiently waiting for the coming of the Messiah. But how would he recognize Him? In that day, as in our own day, there were many spiritual counterfeits. How could Nathanael know? Or how would the Messiah make himself known?
The answer is not hard to find. Jesus revealed his divine knowledge of all things to Nathanael.
Nathanael immediately comes to the proper conclusion: "Rabbi, you are the Son of God; you are the King of Israel" (John 1:49). I feel like I can see Jesus smiling a bit as he replies to Nathanael's eager profession of faith.
God bless Nathanael. Though his faith was imperfect, he rested it on the right object, the Lord Jesus Christ. And Jesus says to him, "You will see greater things than this," meaning that Jesus himself is the one true way to God. He is the "door" to heaven (John 10:9, NASB) and anyone who enters through Him will be saved forever.
So we see in this story Jesus commends the simple faith of an honorable man and then uses that "teachable moment" to reveal enormous spiritual truth that Nathanael would not have completely understood.
Taken from "How Do You Know Me?" by Keep Believing Ministries (used by permission).