What does John 4:54 mean?

According to John 2:11, the turning of water into wine was Jesus' first-ever miracle. That verse uses the Greek word archēn, meaning "beginning," to refer to that event with respect to Jesus' miraculous signs. In other words, this was the very first miracle that Jesus ever performed. He had done no supernatural acts before this.

When this verse refers to the healing of the official's son as "the second sign," it's important to understand the context. This is the "second sign" of John's gospel. It is also specifically referred to as the second sign done by Jesus in Galilee. The first was at the wedding in Cana (John 2:6–11), which also happened to be Jesus' first miracle, period. Between the wedding and the healing of the official's son, Jesus had apparently done many other miraculous works.

The gospel of John records seven "signs," or miracles, intended to prove that Jesus is God. However, John is not claiming that these are the only miracles Jesus ever performed. On the contrary, this book mentions that Jesus did other works which are not specifically recorded (John 20:30–31). It's all but certain that Jesus had performed other miracles while he was in Jerusalem, after the wedding in Cana. Nicodemus referred to His "signs" in John 3:2. People of Jerusalem responded to Jesus' "signs" as well (John 2:23). The fact that the official from Capernaum came seeking healing from Jesus (John 4:46–47) means he had some reason to think that Jesus had miraculous power.