Fourteen teams participated in the 1998–99 Cypriot First Division.
The team with the most points at the end of the season crowned champions.
The last three teams were relegated to the 1999–2000 Cypriot Second Division.
Anagennisi Deryneia, APOP Paphos and Ethnikos Assia were relegated from previous season and played in the 1998–99 Cypriot Second Division.
They were replaced by the first three teams of the 1997–98 Cypriot Second Division, Olympiakos Nicosia, Doxa Katokopias and Aris Limassol.