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Nicknamed 'Luis Figo', he played for local team Lukuli United before moving to Police FC. During the 1996 super divisional league, he emerged as the third top scorer in the league, a factor that altered the big four clubs SC Villa, Express FC, Umeme and Kampala City Council FC to all fight for his signature. At first, he struggled for a place in the starting line-up under coach Paul Hasule but eventually went on to win two 'Doubles' with the club as well as the 1999 Uganda's footballer of the year award. In 2002, he moved to Express FC Red Eagles and became captain of the Ugandan Cup winning side of 2003 and 2006. He left Express FC to join Rwandan outfit APR FC for a short stint, then rejoined Express. He scored 142 league goals between 1997 and 2004, to become the country's top all-time national league top scorer. He has also played for Silkeborg IF in the Danish Superliga. Mubiru is of recent back to Express FC.
In the absence of Turkish based professional Majid Musisi, Mubiru was called to fill the big shoes of Musisi in the group four African Cup of Nations qualifiers encounter between The Cranes and Algeria in 1998. He made a spectacular historical debut in the game, scoring twice, including a memorable last minute strike that gave Uganda a 2-1 victory. Since then, he has played a major part in the national team. He is however criticized for being undisciplined and inconsistent.
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