With four clubs (Cemaes Bay, Flint Town United, Porthmadog and Welshpool Town) all joining in 1998/99 on relegation from the League of Wales, Chirk AAA, Llanidloes Town, Mold Alexandra and Penycae all dropped out of the Cymru Alliance to the three feeder leagues.
When Llandrindod Wells resigned at the league AGM, it appeared that the Cymru Alliance would operate with 18 clubs, but Penrhyncoch then withdrew on the eve of the campaign to join the Mid Wales League and two months later Knighton Town followed suit, but in this case the Bryn-y-Castell outfit took the place of their reserve team in the Mid Wales League (South).
At the beginning of the New Year, Cefn Druids and Porthmadog headed the table, but Glantraeth, with games in hand on the leading duo, were in close proximity and ready to make a title challenge. As the campaign progressed, the Plaskynaston club pulled away at the top as Porthmadog and Glantraeth both faded, whilst champions Rhydymwyn moved through the chasing pack to increase their chances of a top-two finish.
At the end of the season, Cefn Druids were crowned champions by a 12-point margin over the previous incumbents, with Flint Town United and Oswestry Town both finishing nine points behind runners-up Rhydymwyn.
Porthmadog, despite their poor run of form after Christmas, claimed the League Cup with victory over Rhydymwyn in the final. Cefn Druids completed a double when the defeated league rivals Lex XI in the North East Wales FA Challenge Cup final, whilst Welshpool Town lifted the Central Wales Challenge Cup on their return to the Cymru Alliance, when they overcame Cardiganshire League outfit Newcastle Emlyn in the final.
Flint Town United also had a relatively successful campaign, following relegation from the League of Wales, when they reaching the North Wales Coast FA Challenge Cup final, before losing to Bangor City, and also reaching the fourth round of the Welsh Cup, where the Cae Castell club went out at the hands of Port Talbot.