The 1999–2000 Macedonian Second Football League was the eighth season since its establishment.
[1] Due to change of the league structure in season 2000–01, the 19 teams was relegated.
Mesna Industrija promoted to the Macedonian Second League.
Mladost GT Orizari promoted to the Macedonian Second League.
11 Oktomvri promoted to the Macedonian Second League.