Most records indicate that Islam reached Uganda at the very latest in 1844, when Ahmed Ibn Ibrahim reached the then Kabaka`s palace. It is however also believed that some other Arab/Swahili Muslims reached Buganda in the late 1830s, during King Suuna II`s reign . It is also possible that Islam could have reached Uganda earlier through the northern axis, from Egypt and Sudan .what is not under dispute, however, is the fact that Islam arrived in Uganda at least 33 years earlier than Christianity.

Although Islam was not introduced in Uganda through a well?organized missionary system, many people in Buganda including King Mutesa I nevertheless embraced it. Indeed, Islam was taught in the palace of King Ssuuna II. Ssuna even received a copy of the Quran and by the he died , King ssuuna had memorized four chapters of the Quran , Mutesa I, did not convert to Islam but also studied Islam, directed his palace at Banda to become the 1st Islamic Education Center.

The arrival of the Church missionaries Society missionaries (CMS) in Buganda in 1877 and the White Fathers in 1879 heralded a new era. Soon, MutesaI`s belief in Islam was polluted and religious conflicts arose. Eventually religious wars erupted. The Muslims fought bravely although they were finally defeated. On October 12, 1888, they defeated the Christians and forced them out of the capital of Buganda. They ran to Ankole organized and returned. The combined force of Christians, Mwanga and supplies from strokes eventually defeated the Muslims at the battles of Bankaabira, Kitebi and Balwaanyi. The Christians took over Buganda and European influence gained firm ground in the religion-politics of Buganda and eventually Uganda.

Many Muslims made Hijra (migration), too many parts of Uganda hence spreading Islam outside Buganda. The ?Hijra? as the Muslim?s reaction to defeat was later to turn out to be the major achievements of the religious wars. The Muslims turned a defeat into opportunity to sow the seeds of Islam whose frontiers extended well beyond the Buganda Kingdom.

Source :  http://www.moftak.com/Umo/islamUganda.asp