The Vatican today confirmed the November 25-30 trip, saying Francis had been invited by each of the three heads of states and local bishops.
The trip will pose security risks that have largely been absent on Francis' foreign trips to date.
Kenya has been facing the threat of attacks from al-Shabab Islamic militants ever since it sent troops to fight Somali rebels in 2011.
Survivors of the Garissa attack said gunmen targeted Christians and non-Muslims.
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In Uganda, Francis will certainly refer to the Martyrs of Uganda, 45 Anglicans and Catholics killed during the persecution of Christians from 1885-87. Pope Paul VI canonized the 22 African Catholics in 1964.
The Central African Republic, meanwhile, has been rocked by violence since the mostly Muslim Seleka rebel coalition toppled the president in 2013.
The Seleka leader, Michel Djotodia, resigned under intense regional pressure in 2014, and a transitional government is steering the country until a national vote on Oct. 18 - a month before Francis arrives.
Francis is heading to Cuba and the United States next week. With the Africa trip, he will have visited all continents except Oceania in his first three years as pope.