The main talking point surrounded Flint town United, who initially did not take their place in the Cymru Alliance, when the FAW rejected their application to join the North-West Counties League. Despite the Deeside outfit stating that they wouldn't join the new league even if their application to play in England was denied, Flint eventually took their place for the inaugural season. So the first term commenced with Caersws, Carno, Llanidloes Town, Penrhyncoch, Welshpool (all from the Mid Wales League), Gresford Athletic, Lex XI, Mold Alexandra (from the Welsh National - Wrexham Area) Connahs Quay Nomads, Conwy United, Flint Town Utd., Holywell Town and Porthmadog (Welsh Alliance) and Mostyn from the Clwyd League.
The irony of Flint’s decision would not be lost on the rest of the league at the end of the 1990/91 campaign. They were locked in a battle for the championship with Caersws for most of the season, until they visited the Recreation Ground in the last month and prevailed 4-2. Victory at Conwy, in their next fixture, clinched the inaugural title, whilst Caersws had to settle for runners-up spot. Connahs Quay edged out Lex XI for third place after losing to the Deeside outfit in their final league fixture. The Stansty Park club made up for this disappointment by lifting the League Cup with a 2-1 victory over Caersws and claimed the N.E. Wales Cup beating Wrexham Reserves 3-2. Lex also managed to reach the last 16 of the Welsh Cup, before bowing out 4-1 at Bangor City.
The top half of the table was completed by Conwy, Porthmadog and Welshpool, who finished comfortably ahead of the rest. Penrhyncoch had the dubious honour of claiming the first wooden spoon, when the Cae Baker club ended 3 points adrift of Gresford Athletic. Caersws were not to be left empty-handed, as they beat former Mid Wales League rivals Morda United in the CWFA Challenge Cup final. Mostyn reached the Welsh Intermediate Cup final, before losing 2-0 to Welsh League champions Abergavenny Thursdays, their run including a 2-1 victory at the champions in the fourth round.
Flint Town United went on to claim a treble, beating Northern Premier League Caernarfon Town in the NWCFA Challenge Cup final and became the first champions of Wales when they overcame Abergavenny at their former Holywell Road ground in a play-off match between the winners of the two leading domestic leagues