Born in Maastricht, Van den Hoogenband grew up in Geldrop, where he swam for PSV Eindhoven. His father is a team docter with the professional football of the same club. In 1993, he achieved his first successes, performing well on the European Youth Olympic Days.
His international breakthrough came three years later. Aged 18, Van den Hoogenband surprised by finishing 4th in both the 100 and 200 m freestyle at the 1996 Summer Olympics.
After winning no less than 6 gold medals at the 1999 European Championships, he was one of the favourites for the 2000 Summer Olympics, but his adversaries were strong. In the 200 m freestyle, he met Australian youngster Ian Thorpe, favourite of the home crowd in Sydney. In the semi-finals, Van den Hoogenband set a new World Record, but Thorpe countered with a time only 0,02 slower. In an exciting final, Van den Hoogenband equalled his time from the semi-finals to win the gold medal.
In the 100 m freestyle, Van den Hoogenband again set a World Record in the semi-finals and won his second gold medal, defeating the 1992 and 1996 champion, Aleksandr Popov. He won two more medals, both bronze, in the 50 m freestyle and as the final swimmer for the Dutch 4 x 200 m freestyle relay team.
At the 2001 World Championships, Van den Hoogenband won four silver medals in the 50, 100, 200 and 4 x 100 m freestyle events.