The club was founded as part of Ulster Polytechnic in 1972 and entered the Irish League B Division.

On Sunday, 22 February 2015, UU Jordanstown were due to play UCD in the first round of the Collingwood Cup.

However, on Friday, 19 February, just two days earlier, the Irish Universities Football Union barred them from the competition.

Ulster University wanted to enter a single team featuring players from three campuses – Coleraine, Jordanstown and Magee.

However football officials at Coleraine opposed this idea and entered the Collingwood Cup under their own name.