Sixteen teams participated in the 2016–17 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 2016–17 Cypriot Second Division and the last three teams were relegated to the 2016–17 STOK Elite Division.
[4][5] However, after the end of the season Nikos & Sokratis Erimis withdrew from the 2016–17 Cypriot Third Division, and so the 14th-placed team remained to Third Division.
Teams promoted to 2016–17 Cypriot Second Division Teams relegated from 2015–16 Cypriot Second Division Teams promoted from 2015–16 STOK Elite Division Teams relegated to 2016–17 STOK Elite Division