Mr Castro is said to have wanted to visit the pontiff to thank him for his work restoring relations between Cuba and the United States.
Earlier this year Havana and Washington announced they would seek to rebuild diplomatic ties following more than 50 years of tension.
The Holy Father was said to have mediated with both sides urging them to find a common way forward.
The meeting inside the Vatican was "strictly private", officials said, meaning we will never know what was discussed.
Catholic officials had called for the US to lift its trade embargo on Cuba for many years whilst also campaigning for the Cuban government to release Catholics detained in the revolution.