Pope Francis was greeted enthusiastically on Friday as he arrived to meet President Yoweri Museveni at the presidential palace in Kampala
Up to two million people are expected at an open-air Mass at Namugongo, near Kampala, where many of the 45 Anglican and Catholic martyrs were burned alive.
Their execution was ordered by a king worried about Christianity’s spread.
Saturday’s Mass will mark the 50th anniversary of the canonisation of the Catholic martyrs.
Thousands of pilgrims spent the night holding a vigil near the martyrs’ shrines and early on Saturday many more were streaming into the sanctuary, ready for the Pope’s arrival.
Pope Francis is due to pray first at a shrine for 23 Anglican martyrs and then at another shrine marking the spot where another 22 Catholics were killed.
On Friday, the Pope addressed an audience of young people in the Kenyan capital, Nairobi, urging them to unite and take a stand against the destructive effects of tribalism.
On Sunday the Pope will travel to the Central African Republic (CAR), which has been hit by serious violence between Christian and Muslim militias in recent years.