1998–99 Cypriot Third Division

The 1998–99 Cypriot Third Division was the 28th season of the Cypriot third-level football league. Chalkanoras Idaliou won their 1st title.

Format
Fourteen teams participated in the 1998–99 Cypriot Third Division. All teams played against each other twice, once at their home and once away. 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.

Point system
Teams received three points for a win, one point for a draw and zero points for a loss.

Changes from previous season
Teams promoted to 1998–99 Cypriot Second Division
 * AEZ Zakakiou
 * AEK/Achilleas Ayiou Theraponta
 * Anagennisi Germasogeias

Teams relegated from 1997–98 Cypriot Second Division
 * Chalkanoras Idaliou
 * Iraklis Gerolakkou
 * APEP Pitsilia

Teams promoted from 1997–98 Cypriot Fourth Division
 * SEK Agiou Athanasiou
 * ATE PEK Ergaton
 * Doxa Paliometochou

Teams relegated to 1998–99 Cypriot Fourth Division
 * AEK Kakopetrias
 * Kinyras Empas
 * THOI Lakatamia