His is expected to meet President Yoweri Museveni and other senior government officials to discuss and review the activities of the Aga Khan development network in Uganda, a statement from his office says.
He will also meet the Ismaili community in Uganda.
The Aga Khan last visited the East African country in 1997.
He was met at the Entebbe International Airport on Saturday by the Minister of State for International Affairs, Major Tom Butime, and the senior presidential advisor, Dr Martin Aliker.
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