Putin reportedly kept the leader of 1.2 billion Catholics waiting for 70 minutes, a rare occurrence at the Vatican.
Holy See spokesman Father Federico Lombardi said their talks concentrated on the Ukraine conflict and the Middle East, where the Holy See is worried about the fate of the Christian minority.
Developments in Ukraine have resulted in the the pro-western Ukrainian Greek Catholic church pitted against the pro-Russian Orthodox church.
It was the men's second meeting since Francis became pope in 2013.
Fr Lombardi said Francis stressed the need to bring peace to Ukraine through dialogue and implementation of the Minsk accords.
The pontiff also urged access for humanitarian aid.
During the private meeting in the library of the Apostolic Palace, Putin and the Pope exchanged gifts.
President Putin gave Francis an embroidered panel depicting the Christ the Savior Cathedral, while the Pope presented a medallion depicting an angel of peace who brings justice and solidarity.
