Ugyen Academy's first appearance in the national league was in the 2012–13 season, where they finished third behind eventual champions Yeedzin and Drukpol,[2] and were involved in the season's highest scoring game, an 8–1 victory over Samtse.

[2] The following season they won the Bhutan National League, one point above Yeedzin, losing only once, 4–2 to Thimphu City.

[3] By winning the national league, Ugyen Academy were awarded Bhutan's berth in the 2014 AFC President's Cup, their first appearance in any form of continental competition.

They suffered a mediocre start to the season, drawing with eventual winners Druk United and losing to then leaders Thimphu City to find themselves lying in fourth place at the halfway stage.

[5] The team rallied in the second half however, winning all their matches bar a loss to Druk Star to end the season in second place, narrowly losing out on both the title and qualification for the 2015 AFC Cup on goal difference to Druk United.