Fourteen teams participated in the 1999–2000 Cypriot Second Division.
The team with the most points at the end of the season crowned champions.
The first three teams were promoted to 2000–01 Cypriot First Division and the last three teams were relegated to the 2000–01 Cypriot Third Division.
However, in the summer, after the end of the championship, Evagoras Paphos merged with APOP Paphos to form AEP Paphos (AEP took the place of APOP to 2000–01 Cypriot First Division).
Because of this, playoff matches were played between the bottom three teams of 1999–2000 Cypriot Second Division and the fourth team of 1999–2000 Cypriot Third Division (ASIL Lysi), for the extra place in 2000–01 Cypriot Second Division.