San Gwann and Naxxar Lions were relegated from 2006–07 Maltese First Division.The promoted teams from 2006–07 Maltese Third Division were Mgarr United, Sirens and Zurrieq.The league was won by San Gwann.They finished on 47 points, level with Balzan Youths and Rabat Ajax.They were declared champions for their superior goal difference.
They had three points deducted after failing to present the signed balance sheet.
Zurrieq had another two points deducted after being found guilty of casing the incidents which led the BOV Second Division match against Luxol on April 27 to be abandoned.
Referee Chris Francalanza abandoned the match on 69 minutes after he was hit by a Zurrieq player.
Mgarr managed to win the relegation playoffs and secure their second division status for the first time.