Metropolitan Kirill, the head of external relations for the Moscow Patriarchate, said after meeting Benedict that he was increasingly optimistic about relations with Rome.
"It is with great feelings of hope that I leave Rome after this visit," he told Vatican newspaper L'Osservatore Romano after the closed-door meeting.
The Vatican did not immediately release any details about the talks.
The Western and Eastern branches of Christianity have been split since the Great Schism of 1054. Relations between the Vatican and the Russian Orthodox Church, the most important in worldwide Orthodoxy, have suffered particular strain.
Kirill described the meeting with the German-born Pontiff as "very positive and very beautiful", and said it raised hopes that the two Churches could work more closely together to confront shared challenges.
"We need each other ... We are the same family. We share the same Christian values," he said. "Catholics and Orthodox are always more united in confronting the multiple challenges that come from today's world and from secularisation."
Since the break-up of the Soviet Union, the Russian Orthodox Church has accused the Catholic Church of using its new-found freedom to try to win converts there. The Vatican denies charges of proselytising. Kirill was quick to acknowledge that problems remained, but said progress was being made.
"There are steps forward. They're registered from time to time even if problems remain," he said.
Both Vatican and Orthodox officials are open to a possible meeting between Benedict and Russian Patriarch Alexiy II but there has been no indication when such a concrete sign of improving ties could take place.
Kirill recently called on the Vatican to reverse a 2002 decision to create new Catholic dioceses in Russia, something the Russian Orthodox Church see as an infringement on its local territory and power.
Kirill said the Russian Orthodox Church and the Roman Catholic Church were clearly moving closer even if the eventual goal of unity seemed far off now.