Francis, 79, in white robes and a skullcap and Kirill, 69, in black robes and a white headdress, exchanged kisses and embraced before sitting down smiling for the historic meeting at Havana airport.
The 79-year-old pontiff stepped off a plane in the sunshine and shook hands with Cuban President Raul Castro on the tarmac at Jose Marti airport before heading into the meeting with the leader of the powerful Russian branch of the Orthodox church.
The Argentine pontiff is looking to heal a nearly 1,000-year-old rift in Christianity that dates back to a 1054 schism which helped shape modern Europe and the Middle East.
He was due to meet for about two hours with Kirill before embarking on a tour of Mexico.
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The two were due to sign a joint declaration on the contemporary persecution of Christians in places such as Iraq and Syria.
"I just wanted to embrace my Orthodox brothers," said Francis, who became pope in 2013, in an interview this week.
Kirill was on an 11-day trip to Latin America that will also take him to Paraguay and Brazil.