The club was founded in 2012 as formal successor of Zimdra FC, which first recorded involvement in top-flight football in Bhutan in
2011, when they finished as runners-up to eventual winners
Yeedzin in a truncated season consisting of a single round-robin set of matches in anticipation of the commencement of a new
Bhutan National League. The
following season was also reasonably successful. Zimdra again finished as runners-up in the A-Division, this time being beaten to the title by
Drukpol, despite beating Drukpol in the final game of the season. During that campaign, they went through the whole competition unbeaten, dropping points only in a draw with Drukpol and two draws with Yeedzin. finished as runners-up in the
A-Division, winning five and drawing one of their eight games, but finishing five points behind champions Yeedzin. Owner Hishey Tshering was spending a lot of his own money at the time, paying salaries and covering school fees for younger players in a football league where no money is generated from gate receipts and sponsorship is thin on the ground. However, they slipped up in the penultimate round of matches, losing 5–1 to
Druk United. Thimphu had played all their matches and led the league by a point. However, that loss to Druk United meant they were now only a point behind with a game still to play. Druk United thumped Druk Star 8–3 in this final game to take the A-Division title and consign Thimphu to a fourth-straight second place, though they could take consolation in the fact that they had again qualified for the National League. Thimphu City enjoyed a strong start to the 2014 National League season, leading the league at the halfway point, having dropped points only in an opening-day 4–0 defeat to eventual winners Druk United. The second half of the season was less successful. Although they achieved a season-high victory 16–0 against bottom-placed
Bhutan Clearing, they only won one other game and slipped to a final position of third, behind Druk United and Ugyen Academy. == Honours ==