^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 2006–07 First Division, Stranraer were relegated and Partick Thistle 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 2006–07 Second Division, Alloa Athletic won the play-off to stay in the division.
Source: Soccerway Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (C) Champions; (P) Promoted Notes:
^The 2nd, 3rd and 4th placed teams will be entered into a play-off with the Second Division's 9th placed team. The winning team will be awarded a place in the 2006–07 Second Division, Alloa Athletic won the play-off to stay in the division.