The Club won its first trophy, the Edinburgh Shield, in 1883. Historically it is the most successful footballing University in Scotland, winning the Scottish Universities Queen Park Shield 24 times since it donated the trophy in 1921. Edinburgh University also claimed the British Universities Cup in 1994 and continue to constantly qualify for the knock-out stages of the competition.
The most recent achievements of the club include winning the East of Scotland Qualifying Cup in 2005 and finishing in 3rd position in the East of Scotland Premier Division last season. 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 1973. 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 Fife team Cowdenbeath who defeated the University 5-1 at Central Park on 9 December 2006.
With the scrapping of the Scottish Qualifying Cup for the 2007/2008 season under a new Scottish Cup Format, Edinburgh University retain direct entry to the Scottish Cup as a full member of the SFA. Receiving a random bye in the 1st round, Edinburgh University beat Deveronvale F.C. in the 2nd round before losing to Cove Rangers F.C. in the 3rd round. In the 2008/2009 season, Edinburgh University were defeated 1-2 by Civil Service Strollers F.C. in the 1st round of the Cup.