Vatican spokesman Ciro Benedettini said Putin would meet the Argentinian pontiff next Wednesday (June 10).
The Russian leader first met Francis at the Vatican on November 2013, before Russia's March 2014 annexation of Ukraine's Crimea peninsula and the subsequent conflict in the ex-Soviet country's east badly soured relations with Western powers.
The Vatican has adopted a cautious stance on the conflict between Ukrainian authorities and pro-Russian rebels in eastern Ukraine which has religious overtones.
Francis has publicly voiced his frustration over "a war between Christians," but has not heeded calls from leaders of Ukraine's minority Greek Catholic community to firmly condemn Russia's actions in Ukraine.