The Maltese Second Division 2006-07 (known as BOV Second Division 2006-07 due to sponsorship reasons) started on 23 September 2006 and ended on 6 May 2007. Lija Athletic and St.Andrews were the relegated teams. The promoted teams were Birzebbuga St.Peters, Santa Venera Lightning and Rabat Ajax. Dingli Swallows finished the league as champions. Therefore, they were promoted to 2007–08 Maltese First Division. They were joined with Mellieha who finished as runner-up. Gudja United and Gozo FC were relegated to 2007–08 Maltese Third Division. Zebbug Rangers were also relegated as they lost the relegation-playoffs.

Participating teams

Changes from previous season

Final standings

Relegation playoffs

Top scorers

Results