The conflicts between the Pharisees and Jesus are recurring in the gospels, but not every Pharisee had issue with Jesus.
Enter Nicodemus. He is actually "a ruler of the Jews" (3:1), which is a pretty important position. Nicodemus knew from the surprising acts (as described in 2:23) that Jesus must have some relation to God. The miracles are meant to be acts of God, after all.
Nicodemus decided to come to Jesus "by night" (3:2). It's likely that Nicodemus didn't want to face controversy with other Pharisees by going in day, so he tried to keep the meeting as secret as possible. Nevertheless, he still came to learn from Jesus.
Jesus knew that Nicodemus wanted to learn from him, so Jesus told Nicodemus something important -- that people "cannot see the kingdom of God" until said person "is born again". Later in the conversation and after some questions from Nicodemus, Jesus would explain what all that means.