Runje began his professional career at Hajduk Split in 1996, but was unable to become a regular at the firstly team with first Tonci Gabric, the Croatian national team's back-up goalkeeper at the time, and young prospect Stipe Pletikosa being selected ahead of him. He left the club in 1998 and joined Belgian side Standard Liège.

1996–1998 Hajduk Split
1998–2001 Standard Liège
2001–2004 Marseille
2004–2006 Standard Liège
2006–2007 Besiktas
2007–2011 Lens