Fourteen teams participated in the 1990–91 Cypriot Second Division. All teams played against each other twice, once at their home and once away. The team with the most points at the end of the season crowned champions. The first two teams were promoted to 1991–92 Cypriot First Division. The last two teams were relegated to the 1991–92 Cypriot Third Division.
The 3rd-placed team faced the 12th-placed team of the 1990–91 Cypriot First Division, in a two-legged relegation play-off for one spot in the 1991–92 Cypriot First Division. The 12th-placed team faced the 3rd-placed team of the 1990–91 Cypriot Third Division, in a two-legged relegation play-off for one spot in the 1991–92 Cypriot Second Division.
Teams received two points for a win, one point for a draw and zero points for a loss.
Teams promoted to 1990–91 Cypriot First Division
Teams relegated from 1989–90 Cypriot First Division