 The first three teams were promoted to the 2000–01 Cypriot Third Division and the last three teams were relegated to regional leagues.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 in the 2000–01 Cypriot First Division.Because of this, playoffs between the bottom three teams of the 1999–2000 Cypriot Second Division and the fourth team of the 1999–2000 Cypriot Third Division were held for the extra place in the 2000–01 Cypriot Second Division.