Ilsanker started his career with his local club, SK Hallein. Then he went to SV Austria Salzburg where he spent most of his active career (1993 to 1998). For Salzburg he played 98 matches. From 1998 until the end of his career in 2001 he played with the German team 1. FSV Mainz 05. His teammate there was Jürgen Klopp, who is now coach of Borussia Dortmund.