The FAW Premier Cup began its life as the FAW Invitation Cup in season 1997/98 before changing to its present title when the separate company that operates the competition, the FAW Premier Cup Ltd, negotiated a new three-year contract with BBC Wales for the television rights. A one-year contract with a revised format for the 2001/2002 season was replaced by a new two-year deal for seasons 2002/2003 and 2003/2004. Another revised format one year contract was agreed for 2004/2005 and 2005/2006, which has just been renewed for seasons 2006/2007 and 2007/2008.

The original FAW Invitation Cup consisted of 8 teams, who were; Cardiff City, Swansea City, Wrexham, Merthyr Tydfil, Barry Town, Bangor City, Newtown and Cwmbran Town but when the new contract was agreed the number increased to 12, with 4 more LOW clubs joining. This continued with the contract for the seasons 2002/2003 and 2003/2004. The contract for 2004/2005 and for the current season see 16 clubs involved with 11 from the Welsh Premier League, the 3 Football League clubs and the two with the best previous season playing record from Colwyn Bay, Merthyr Tydfil and Newport County.

The inaugural winners were Wrexham F.C. who beat Cardiff City F.C at the Racecourse by 2-1. In the 1998/99 season, Barry Town FC defeated Wrexham FC at the Racecourse. Wrexham FC reclaimed the trophy in 1999/2000, beating Cardiff City at the Racecourse by 2 - 0 and they retained it in 2000/2001 when they overcame Swansea City at the Vetch by 2-0. The 2001/2002 season saw Cardiff City win the trophy for the first time in a passionate local derby with Swansea City when Kavanagh's solitary goal proved decisive. In 2002/2003, it was a return to the Robins, as Wrexham again claimed the trophy with a comprehensive victory over Newport County by 6-1, and 2003/2004 saw them win again at Rhyl by 4-1. However, the 2004/2005 season saw a change as Swansea claimed the trophy for the first time with a 2-1 win over Wrexham in the last ever game at the "old" Vetch Field. Swansea again retained the title in 2005/2006 with another 2-1 win over Wrexham, but this time at the Racecourse.

In 2006/2007, for only the 2nd time in the competition's history, the trophy was claimed by a Welsh Premier League club as The New Saints F.C. overcame Newport County by a solitary goal.

Finally it was third time lucky for Newport County as they won the 2007/08 Final 1-0 overcoming Llanelli in a disappointing match that was spoilt by the elements.