It started in September 2008 and ended in late May 2009, with the promotion play-off finals.
The winners from both sections will face each other in a play-off where the winner is crowned as champion of this division, but both teams will still be given promotion to the Second Division.
Gharghur were the winners of Section A, while Gzira United were the winners of Section B. Gzira United finished the season as overall champions after they beat Gharghur 3–0.
Zurrieq were also promoted after winning the promotion play-offs, beating Santa Lucia on penalties in the final.
Santa Lucia beat Naxxar Lions in the semi-final.