It comes little over a week after their manager Ryan Docherty departed the role.
They cited a lack of players as their reason to coming to the decision.
While they hoped they would be able to continue, they added they felt it was of higher importance to ensure what players remained could continue their development in a more suited environment elsewhere.
It brings to an end an era of around six years for the club – who have competed in the Scottish Lowlands Development Football League for the past two seasons.
Thistle were one of few teams to survive in their conference last season – in which around half of the teams involved at the beginning of the campaign ultimately withdrew.
However, this season, it is now the Stevenston side who will not complete their season in Conference F.
The club confirmed the decision with a statement earlier today, February 9.
It said: “The club can announce that the Under 20s development squad have withdrawn from the league for the remainder of the season.
“The remaining players were informed of the decision last night.
“Unfortunately despite everyone at the team’s best efforts, we just didn’t have enough players to keep the team going and decided it was more important to get the remaining players back playing and enjoying their football.
“We would like to thank everyone involved for their efforts for this season, and thank you to the players who stayed until the end. Their loyalty will not be forgotten.”
The youth pathway has proved fruitful for Ardeer’s first team to date, with numerous players from their under 20 side pushing into Sean Kenney’s squad.
This was exhibited perfectly on Saturday – where six of the first team’s starting 11 against Glasgow Perthshire were current, or former, under 20’s players.