1999–2000 Macedonian Second Football League

The 1999–2000 Macedonian Second Football League was the eighth season since its establishment. It began in August 1999 and ended in May 2000. Due to change of the league structure in season 2000–01, the 19 teams was relegated.

Relegation playoff
Shkëndija Arachinovo were won the match and stayed in the Macedonian Second League, while Tiverija were relegated to the Macedonian Third League.

Mesna Industrija were won the match and promoted to the Macedonian Second League.

Mladost GT Orizari were won the match and promoted to the Macedonian Second League.

11 Oktomvri were won the match and promoted to the Macedonian Second League.

Source: Nova Makedonija