Born in Rijswijk, Knopper began his career with Feyenoord but, still in his youth, moved to rivals Ajax, making his official debut in November 1997 against Sparta Rotterdam.

In 1999, he was voted by club supporters as Most Talented Player, receiving the Marco van Basten Trophy; the following year he scored 15 Eredivisie goals as a midfielder, but his team could only finish fifth.

[1] From 2002 to 2004, he went out on two loans, first with Greece's Aris and then with Heerenveen, slightly reviving his career with the latter; upon his Ajax release in summer 2004, he spent two additional campaigns with Vitesse, appearing regularly.

In July 2007 a three-year contract was agreed, with the player netting again in double figures (ten) in 2008–09, crucial to help in a narrow escape from relegation; in the 2010 summer, aged 33, he was released.

In January 2011, Knopper moved to Liga Primer Indonesia club PSM Makassar, leaving after a couple of months and signing with lowly Haaglandia back in his country, where he ended his career.