Bukedi came from behind to out-muscle Tooro 2-1 during group B of the quarter finals in the FUFA Drum during match day two at the Pece war memorial stadium.
Anwar Ntege, a Uganda Revenue Authority (URA) scored the opening goal for Tooro just after 10 minutes.
Bukedi quickly responded to find the equaliser through Ibra Nsimbe five minutes later.
Team skipper Fredson Gwoto of Jinja based side Bul fc put Bukedi into the lead in the 36th of the game.
Ibrahim Pengere of Bukedi was named man of the match, earning a 100,000 shillings prize.
Bukedi now leads group B since the second game on the day witnessed Acholi overcome the reigning champions Buganda 1-0 in a well contested game.
Tito Okello scored the lone goal on the evening graced by hundreds of spectators.
Action returns with match day three of the quarter finals with two matches at Akii-Bua stadium in Lira.
Lango takes on Busoga in the opening match at 2pm and Bugishu will face West Nile in the subsequent game.