 Also, playoffs between the bottom three 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.Teams received three points for a win, one point for a draw and zero points for a loss.Teams promoted to 1999–2000 Cypriot Third Division

Teams relegated from 1998–99 Cypriot Third Division

Teams promoted from regional leagues

Teams relegated to regional leagues