The meeting is taking place at the Kremlin along with Tillerson's counterpart, Russian Foreign Minister Sergey Lavrov, the U.S. State Department and Putin's spokesman Dmitry Peskov confirmed, CNN reported.

The talks come after Lavrov issued Tillerson a warning Wednesday against any further U.S. strikes on the Syrian regime. Russia is Syria's most powerful ally.

Read alsoPutin complains of degradation of ties with U.S. under TrumpThe two top diplomats had sat down together earlier in the day to work through the fallout of last week's chemical attack in northwestern Syria, which plunged the old Cold War enemies to a new low.

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Putin has traditionally met with the U.S. Secretary of State on their visits to Moscow. And Tillerson and Putin are no strangers – Putin in 2013 awarded the Order of Friendship to Tillerson when he was CEO of ExxonMobil, the highest honor Russia gives to foreigners.

An icy welcome

Lavrov gave Tillerson an icy welcome Wednesday, diving straight into Moscow's grievances with Washington in what would usually be warm opening remarks.

Russia "saw some very troubling actions regarding the attack on Syria," he said, according to an official Russian interpreter.

"We believe it is fundamentally important not to let these actions happen again."

The White House on Tuesday accused Russia and Syria of carrying out a confusion campaign over who was responsible for the chemical attack. Russian President Vladimir Putin has made comparisons between the U.S. response and its 2003 intervention in Iraq, calling it a "tedious" story.

Moscow and Washington have traded barbs over last week's chemical attack, which killed 89 people, and prompted the U.S. to carry out its first strike against the Syrian regime in the six-year conflict, taking out aircraft and infrastructure at a Syrian military air base.