Putin and Pompeo both said that the two countries are willing to mend ties and build up cooperation, after the meet.
Before a closed-door meeting with Pompeo, Putin said on Tuesday, he had an impression from a phone call with US President Donald Trump on May 3 that the latter is willing to restore US-Russia relations and jointly resolve issues of mutual interest, Xinhua reported.
"For our part, we have repeatedly said that we would also like to restore the relationship in full format. I hope that now the necessary conditions are being created," Putin told Pompeo.
Praising the probe by Robert Mueller, Putin said "Despite the exotic nature of Mr Mueller's commission, on the whole he conducted quite an objective investigation and confirmed the absence of any collusion between the US administration and Russia.”
Moscow has rejected these claims "from the very beginning as complete nonsense".
Pompeo earlier told Russian Foreign Minister Sergei Lavrov that US President Donald Trump was committed to improving relations with Moscow.
Pompeo underlined to Putin that Trump wanted to make "our two peoples more successful and, frankly, the world more successful, too."
"President Trump wants to do everything we can and he asked me to travel here to communicate that.
"Some of our cooperation has been excellent - on North Korea, on Afghanistan, we've done good work - (and) counter-terrorism work - together. These are things we can build upon,” said Pompeo.
Pompeo said that Washington and Moscow have different positions on some issues, but they also share interests and have potential to cooperate and work productively.
After the meeting, Kremlin aide Yuri Ushakov said Pompeo told Putin that Trump is ready to hold talks with the Russian leader during the G20 summit in Japan's Osaka in June.