Stojkovski started his career playing with his home town club FK Pelister, back then playing in the Yugoslav Second League. In 1991 his skills were noted and he moves to the 1991 European Champions Red Star Belgrade where he stayed 4 seasons and played over 120 games. In the legendary 100th eternal derby against their greatest rivals Partizan, he scored and was named the man of the match. In 1995, he signed with Spanish La Liga club Real Oviedo where he played 67 league matches in two seasons with the side. In 1998 VfB Stuttgart signed him and he was part of the team that reached the 1998 UEFA Cup Winners' Cup Final where they lost against Chelsea. After two and a half years in Germany, he returned to Pelister where he retired in 2001 by winning the Macedonian Cup that year.