[4] More details are available for the following season, where Transport United finished third, four points behind winners Drukpol, winning five and drawing one of their eight games in the single round-robin competition.

[6] Their success in the prior season continued in 2005 as they won their second consecutive A-Division title,[7] winning nine and drawing two of their twelve games[7] and qualifying in the process for the 2006 AFC President's Cup.

[10] This time, having travelled to Kuching, Malaysia where the tournament was being held, Transport United performed slightly better, losing in their first game to Khemara, only thanks to a last minute goal from Kim Son-U, when it had looked like Ugyen Wangchuk's equaliser would be enough to secure their first point.

Details for this season are also scant, but in the game between Transport United and RIHS FC, Passang Tshering scored seventeen goals.

[12] The team got off to the worst possible start, conceding 13 against Regar-TadAZ and 6 against Ratnam SC, with only Gyeltshen's goal against the Sri Lankans providing any sort of comfort.

[14] Once again, having travelled to Colombo where all the group games were scheduled to take place, the club got off to a bad start losing 7–1 to both Aşgabat and Ratnam SC before capitulating 11–0 to Kanbawza to leave the competition with three losses, 25 goals conceded and only two scored.

The club's form slumped in 2009 as they won only three games and drew five to finish in fifth place out of eight teams, suffering 10–1 and 7–2 defeats at the hands of Yeedzin and Druk Star respectively.

[15] An improvement the following season saw them finish in third place, behind Drukpol on goal difference, but nine points behind winner Yeedzin, winning eight and drawing one of their twelve games.

[17] The next season, for the first time in their history, Transport United were relegated,[18] finishing in second to last place, with their only points coming from two victories over bottom-placed team Nangpa.