Vatican spokesman Greg Burke, briefing reporters on the trip, said that he would meet the head of the army, Senior General Min Aung Hlaing, on the morning of Nov 30 in a church residence in Yangon.
Myanmar Cardinal Charles Maung Bo had talks with the pope in Rome on Saturday and suggested that he add a meeting with the general to the schedule.
Both the pope and the general agreed.
Myanmar's government has denied most of the claims, and the army last week said its own investigation found no evidence of wrongdoing by troops.
Burke said that "a small group" of Rohingya refugees will be present at an inter-religious meeting for peace in the Bangladeshi capital, Dhaka on the afternoon of Friday, Dec 1.
He gave no details of how they would be chosen.
Both events were not on the original schedule of the trip of the Nov 26-Dec 2 trip.
Some 600,000 Rohingya refugees, most of them Muslim and from Myanmar's northern Rakhine state, have fled to Bangladesh.