The 2008–09 Maltese Second Division season, also known as the 2008–09 BOV 2nd Division due to sponsorship reason) started on 27 September 2008 and ended on 10 May 2009.
The promoted teams were Gozo FC and Zebbug Rangers.
The 2008–09 Maltese Second Division was won by Balzan.The runners-up were Melita, who finished 2 points off Lija Athletic.
Mgarr United and Marsa were relegated to the Third Division.
Naxxar Lions were also relegated as they lost in the promotion-relegation play-offs to Santa Lucia.