Fourteen teams participated in the 1999–2000 Cypriot Third Division.
The team with the most points at the end of the season crowned champions.
The first three teams were promoted to the 1999–2000 Cypriot Second Division and the last three teams were relegated to the 1999–2000 Cypriot Fourth 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 in the 2000–01 Cypriot First Division.
Also, playoffs between the bottom 3 teams of the 1999–2000 Cypriot Third Division and the fourth team of the 1999–2000 Cypriot Fourth Division were held for the extra place in the 2000–01 Cypriot Third Division.