During a trip to Italy, the Muslim leader spent 40 minutes speaking with the Holy Father at the Vatican.
At the end of the discussions, Mr Rouhani said: "I ask you to pray for me."
He said the trip to the seat of the Catholic Church had been a "a real pleasure".
Francis told the president he "hoped for peace" following the meeting which it's reported focused heavily on the Syrian civil war.
He gave Mr Rouhani a St. Martin medal which he said was "a sign of unsolicited brotherhood."
The meeting was made possible following the landmark deal signed on Iran's nuclear ambitions.