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.
The promoted teams were Birzebbuga St.Peters, Santa Venera Lightning and Rabat Ajax.
Dingli Swallows finished the league as champions.
Gudja United and Gozo FC were relegated to 2007–08 Maltese Third Division.
Zebbug Rangers were also relegated as they lost the relegation-playoffs.