Leko started his career with his hometown club Hajduk Split and played there for several seasons before moving to Spain to join Málaga CF. In January 2005, Leko returned for a brief stint with Hajduk; in the summer he joined Club Brugge. On 15 January 2009, he decided to sign a contract for K.F.C. Germinal Beerschot. After his spell at the Antwerp side, he went on with his career at K.S.C. Lokeren. Todays he is head coach of Hajduk Split.

2x Croatian Championship (2000/2005) [Hajduk]
1x Croatian Cup (1999) [Hajduk]
1x UEFA Intertoto Cup (2002) [Malaga]
2x Belgian Cup (2006/2011) [Brugge/Lokere]