The Mounties program has been in continuous operation since 1955 when they played an exhibition schedule and then officially joined the New Brunswick Football League (NBFL) in 1956.

[4][5] In June 2008, Kelly Jeffrey was named interim head coach for the 2008 season and led the Mounties to a berth in the playoffs for only the second time in the new millennium.

[6] Another 0–8 season in 2011 was followed up by a successful 2012 which had the Mounties in the playoffs again, and boasted the AUS leading rusher (Jordan Botel) and the emergence of a new leader at quarterback, freshman Brandon Leyh.

Brady was the first permanent head coach in the program's recent history who was both a Mount Allison graduate and former player for the Mounties.

They would defeat the Acadia Axemen 27–18 to compete in their fourth straight Loney Bowl but would end up losing to the St. Francis Xavier X-Men 29–8.

In 2019, Mount Allison brought in former CFL player and Acadia Axemen alumnus Kyle Graves to take over as Offensive Coordinator.

The team lost their first four games of the season, but then won their next three and eventually finished with a 3–5 record and enough to qualify for the playoffs but fell short in the first round to the Bishop’s Gaiters in their second year in the AUS conference.

The post-season would prove to be much different for the Mounties squad as they were able to defeat their recent nemesis the Bishop’s Gaiters in Lennoxville, Quebec bringing them to the Loney Bowl for the first time since 2016.

Following this defeat in the AUS Championship, the Mounties have seen a dramatic decline in their performance with the graduation of many of their key contributors to their previously dominant defence.