Edinburgh University are eligible to compete in the Scottish Cup every season as they are full members of the SFA.

A group describing itself as "The Edinburgh University Foot Ball Club" played three matches in 1851.

In October 2006, the side beat Vale of Leithen 3–0 to reach the first round proper of the Scottish Cup for the first time since 1972–73.

In November 2006, they defeated Keith to proceed to the second round of the Scottish Cup for only the second time in the club's history, and 106 years after their first appearance at this stage.

The team's 2006 cup run was halted by Cowdenbeath, who defeated the university 5–1 at Central Park on 9 December 2006.