Vatican spokesman Ciro Benedettini said Putin would meet the Argentinian pontiff in the afternoon of Wednesday June 10th.
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.
In February, he rankled Ukraine’s Greek Catholics after calling the conflict “fratricidal".
“It’s fair to say that many Greek Catholics in Ukraine have not felt adequately supported by Pope Francis," John L. Allen Jr, associate editor of the Boston Globe and Vatican specialist, told The Local, adding that the meeting with Putin could go one of two ways.
"It will either be another confirmation for the Greek Catholics that the Pope is more concerned about a broader geopolitical cooperation with Russia, as it is aligned on issues such as Syria and protecting Christians there, or it will be an opportunity for him to do a balancing act in deepening the seas to use the opportunity to show Greek Catholics that he has their backs."
The visit is being tagged on to the end of Putin's scheduled trip to Milan to attend the World Expo, which the Kremlin announced on Monday.
Italy, the second-largest trade partner in the EU with Russia, has been softer in its stance towards sanctions against the country over the Ukraine conflict.
Premier Matteo Renzi also sought Russia's help with resolving the Libya crisis.
Russia's economy has been hit hard by the sanctions, while a Russian embargo on food imports has had a huge impact on Italian exporters.