The two men spoke for nearly an hour in the pope's library in the Apostolic Palace.
After they emerged from their closed-door talks, Mr Macronput a hand on Francis' shoulder, and then kissed him on both cheeks.
Francis reciprocated the warmth, gripping the French leader's arm and then shaking his hands vigorously and smiling broadly as he said goodbye. He also shook hands with Mr Macron's wife, Brigitte.
As is his custom with guests, Francis gave Mr Macron a medal depicting St Martin of Tours, who gave his cloak to a poor man.
Francis had ushered the French leader into his studio, where the two men chatted for a few minutes before the media were escorted out of the room.
Last week, the pontiff urged nations to welcome all the refuges they can properly manage. Italy is angry that France sends back migrants who illegally enter France from Italy.
France recently criticised Italy's new populist government for refusing to allow docking by a private rescue ship with more than 600 migrants aboard. Spain eventually gave the ship safe harbour.
Mr Macron's visit was strictly Vatican-related, with no meetings scheduled with Italian leaders.
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