The Pope was on a mission of reconciliation in the Balkans in his second visit to the region to promote tolerance in the Serb-dominated half of the country where Catholics and Muslims are a minority.
Deutsche Welle reported that the Pope's visit had been opposed by Banja Luka's Serbian Orthodox majority.
They were further angered by the fact mass was celebrated in a Franciscan monastery near which troops led by a priest killed some 2,000 Serb villagers during World War II.
The BBC reported that the mass drew 50,000. Fifty years after World War II Serbs forced Bosnian Croats and Muslims to flee Banja Luka as Yugoslavia fell apart.
The visit was not marred by violence or demonstrations as had been feared.