It was won for the third time by Linlithgow Rose after they defeated Kelty Hearts 2–1 in the final.
Under a new rule change, the Junior Cup winners (along with winners of the North, East and West regional leagues) qualify for the senior Scottish Cup; Linlithgow Rose therefore competed in the 2007–08 Scottish Cup.
These ties were scheduled to take place on Saturday 30 September 2006.
These ties were scheduled to take place on Saturday, 2 December 2006.
These ties were scheduled to take place on Saturday 10 February 2007.