The whole of the verse in John 3:13 reports Jesus’ words to Nicodemus this way:
“No one has ascended into heaven, except he who descended from heaven, the Son of Man.”
The KJV adds the words, “which is in heaven.” Even without this addition it is clear that Jesus is not talking about his geographic position on earth or in the sky, but is referring to his close relationship with his Father. To say that he descended from heaven is to say that he was sent by God. His teaching was not his own, but his Father’s. He says, in John 7:16, “My teaching is not mine, but his who sent me.” Jesus was not the only one who was sent by God. Of John the Baptist we read, in John 1:6, “There was a man sent from God, whose name was John.”
So, the sense in which Jesus descended from heaven is that he had been sent by God.
A parallel passage is John 6:38:
For I have come down from heaven, not to do my own will but the will of him who sent me.
This statement confused the Jews who were listening to Jesus:
John 6:42 They said, “Is not this Jesus, the son of Joseph, whose father and mother we know? How does he now say, ‘I have come down from heaven’?”
In response, Jesus explained that he was like the manna in the wilderness which “came down from heaven” (John 6:48-51). The manna didn’t physically fall like snow — it was more like frost (Exodus 16:14-15) which formed on the ground. But, like Jesus, it had been sent by God.
In a somewhat similar way, Matthew often reports Jesus as speaking about the kingdom of heaven. This does not mean the kingdom is in heaven, but that it is God’s kingdom, and in the other gospels it is called the kingdom of God.