Before the establishment of Malaysia on 16 September 1963, the tournament was contested by three national teams, North Borneo, Sarawak and Brunei.

The following year, the tournament served as the Malaysia Cup east zone qualifying round.

[2] In the 2010s, there is an effort to revive the Cup by the Sabah Football Association (SAFA), but with the absence of sponsors and the tight schedule of the Brunei team in the S.League became a major barrier to the efforts.

The Sabah team then won another 12 titles from 23 Borneo Cup editions until 1988.

In 1989, the Borneo Cup was abolished after the failure of the team to conclude an agreement with FAM to join the Semi-Pro League.