Macron made the visit to accept an inherited title of Honorary Canon of the Basilica of St. John Lateran.
Pope Francis and Macron exchanged gifts, Vatican News reported. Macron's wife, Brigitte, accompanied him at the papal audience.
The pontiff gave Macron, who was baptized a Catholic at age 12, a medallion of St. Martin of Tours, which shows Martin on horseback cutting his cloak in two to give part to a beggar in winter.
Macron gave the pope a rare copy of Georges Bernanos' 1936 book, Diary of a Country Preist.
Pope Francis and Macron discussed a range of diplomatic issues for more than an hour -- including environmental protection, migration, and conflict prevention and resolution, particularly disarmament, a Holy See Press Office Communique said.
The leaders' dialogue on conflicts focused on areas in the Middle East and Africa.
Macron also met with Cardinal Secretary of State Pietro Parolin and Archbishop Paul Richard Gallagher, Secretary for Relations with States.
Later, he accepted the title of First and Only Honorary Canon of the Basilica of St. John Lateran. The tradition of French heads of state inheriting the title dates back to 15th century French monarchy.