Chalkanoras Idaliou won their 1st title.
Fourteen teams participated in the 1998–99 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.
Teams promoted to 1998–99 Cypriot Second Division Teams relegated from 1997–98 Cypriot Second Division Teams promoted from 1997–98 Cypriot Fourth Division Teams relegated to 1998–99 Cypriot Fourth Division