The club was founded in 1998 KF Gostivar. not to be related with KF Gostivar 1919 which was disloved in 2010.
In the 2012–13 season, Gostivar finished second and was promoted to the Macedonian First League for the first time in club history.
Its first win in 2013/14 season was on 18/08/2013 against FK Rabotnički. Gostivar’s defender Ekrem Hodžić scored two goals contributing in the 2–0 win.