The 80-year-old pope, the first to travel to Myanmar, received Senior General Min Aung Hlaing for a 15-minute meeting at the archbishop's residence in Yangon, where the pontiff is staying during his visit.
At least 620,000 Rohingya have fled western Rakhine state to Bangladesh, describing rape, murder and arson at the hands of Min Aung Hlaing's army and ethnic Rakhine Buddhist mobs.
The UN and US have accused the military of "ethnic cleansing" in a campaign sparked by attacks by a militant Rohingya group on police border posts in late August.
The army chief told the pope that "Myanmar has no religious discrimination at all. Likewise our military too [...] performs for the peace and stability of the country", according to a Facebook post published by the general's office a few hours after the meeting.
There is also "no discrimination between ethnic groups in Myanmar", he added.
