But he wasn't welcome everywhere.
Russia refused to invite the Polish-born pontiff, accusing the Catholic Church of seeking to undermine Russian Orthodoxy through aggressive proselytizing.
Since John Paul's death and Benedict's election in the spring of 2005, however, there have been signs of a thaw.
A high-ranking Catholic envoy has held talks in Moscow with Patriarch Aleksy II, the head of the Russian Orthodox Church. Benedict himself has called the millenium-old division of the two churches a "scandal."
It's unlikely, however, that Putin will use his first meeting with Benedict to extend an invitation to the pontiff to visit Russia.
"I think the Vatican doesn't expect much from this meeting in terms of ecumenical dialogue," said Paolo Rodari, Vatican correspondent for Italy's "Il Riformista" newspaper. "I'm not sure the talks between Putin and the pope will contribute to a future meeting between the two churches. The pope will continue to develop his relations with the Russian Orthodox Church directly through Aleksy II and the Moscow Patriarchate. I don't think that Putin will offer the pontiff an invitation to come to Moscow, as [former Soviet leader Mikhail] Gorbachev did."
The two churches share mutual concerns about growing secularism and the rise of radical Islam.
But Rodari says Putin, despite his own professed religious beliefs, is approaching today's Vatican meeting as a head of state -- not as a representative of Russian Orthodoxy.
"He and the pope will discuss issues related to Russia, Islam, the situations in Kosovo, Chechnya, the Middle East," Rodari said. "I think the discussion will be more about international politics than about religion."
The two men are expected to speak German -- the pope's native tongue and the language spoken by Putin during his years as a KGB officer in former East Germany.