The 78-year-old pontiff was given a rapturous welcome as he flew in to the central town of Entebbe, heading straight to Uganda's presidential palace in a small hatchback car as waving crowds gathered along the roadside, four deep in some places.
In his opening speech, Francis said his visit was "meant to draw attention to Africa as a whole: its promise, its hopes, its struggles and its achievements.
"The world looks to Africa as the continent of hope," he said.
The pope has made humility and help for the impoverished a hallmark of his tenure.
Also Read
Veteran Ugandan leader Yoweri Museveni, widely expected to be re-elected next year for his third decade in power, said he was honoured to host Pope Francis, describing his compassion for the poor and his frankness of spirit as "an encouragement for all of us."
In his address, Francis hailed Uganda's "outstanding" response in welcoming some half a million refugees and enabling them "to rebuild their lives in security and with a sense of dignity."
"How we deal with them is a test of our humanity, our respect for human dignity, and above all our solidarity with our brothers and sisters in need."
On the eve of his arrival, Ugandan MPs passed a controversial bill handing the authorities sweeping powers to supervise, approve, inspect and dissolve NGOs in a move which could see rights activists jailed for documenting abuses.
Rights groups say the move is likely to "strangle" criticism of the government.
Francis later headed to a shrine at Munyonyo, near the capital Kampala, where in 1886 the Ugandan king ordered the execution of more than 40 Protestant and Catholic Christians, who are revered as martyrs.