Anagennisi Deryneia won their 1st title.
Fourteen teams participated in the 1998–99 Cypriot Second Division.
The team with the most points at the end of the season crowned champions.
The first three teams were promoted to 1999–2000 Cypriot First Division and the last three teams were relegated to the 1999–2000 Cypriot Third Division.
Teams promoted to 1998–99 Cypriot First Division Teams relegated from 1997–98 Cypriot First Division Teams promoted from 1997–98 Cypriot Third Division Teams relegated to 1998–99 Cypriot Third Division