Forfar Athletic were relegated to the Third Division while Stranraer enter the promotion/relegation playoffs with the second, third and fourth placed teams of the Third Division - Arbroath, Queen's Park and East Fife respectively.
Source: "2006–2007 Second Division - SPFL Archive". SPFL (in Malay). Retrieved 2021-04-29. Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (C) Champions; (P) Promoted; (R) Relegated Notes:
^The 2nd, 3rd and 4th placed teams will be entered into a play-off with the First Division's 9th placed team. The winning team were awarded a place in the 2007–08 First Division, Airdrie United were relegated and Stirling Albion were promoted.
^The 9th placed team were entered into a play-off with the Third Division's 2nd, 3rd and 4th placed teams. The winning team were awarded a place in the 2007–08 Second Division, Stranraer were relegated and Queen's Park were promoted.
The ninth placed team in the Second Division played the fourth placed team in the Third Division and third placed team in the Second Division played the second placed team in the Second Division. The play-offs were played over two legs, the winning team in each semi-final advanced to the final.
