The Russian Orthodox Church said the “persecution of Christians” would be the central theme of the historic meeting.
Pope Francis will stop over in Cuba on his way to Mexico.
It is the first papal meeting with a Russian Church head since the Western and Eastern branches of Christianity split in the 11th Century.
The meeting is due to take place at Havana airport, where Pope Francis and Patriarch Kirill will sign a joint declaration.
Patriarch Kirill is due in Cuba for an official visit at the same time as Pope Francis’ stopover in Havana.
In a joint statement, the two churches said the meeting would “mark an important stage in relations between the two churches”.
They invited “all Christians to pray fervently for God to bless this meeting, that it may bear good fruits.”‘
Since becoming Pope in 2013, Francis has called for better relations between the different branches of Christianity.
The foreign policy chief of the Russian Orthodox Church, Metropolitan Illarion, told reporters that there were still differences between the two churches, but that international events had pushed the leaders to meet.
Metropolitan Illarion said: “The situation in the Middle East, in northern and central Africa and in other regions where extremists are perpetrating a genocide of Christians, requires immediate action and an even closer cooperation between Christian churches.
“In this tragic situation, we need to put aside internal disagreements and pool efforts to save Christianity in the regions where it is subject to most severe persecution.”
Patriarch Kirill has been the head of the Russian Orthodox Church since February 2009, while Pope Francis took up his role in March 2013.
The Roman Catholic Church has more than a billion members worldwide, while the Russian Orthodox Church numbers about 165 million.
The Orthodox Church is made up of more than 10 separate churches. The Vatican has existing ties with the Istanbul-based Ecumenical Patriarch, Bartholomew I, but this will be the first meeting between the Pope and the patriarch of the Russian Church, which is the largest and most powerful Church in Orthodoxy.
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