"They will discuss ongoing efforts to achieve a political transition in Syria," spokesman Mark Toner said on today on the sidelines of the UN climate summit in Paris.
The Russian foreign ministry said it hoped the visit, Kerry's second this year, would improve what it said were the "complicated" relations between the rival capitals.
The talks will also cover differences in the parallel Russian and US approaches to the fight against IS.
The Kremlin insists its ally in Damascus has the sole right to authorise foreign military intervention against the jihadists and US bombing violates Syrian sovereignty.
And the US envoy will also bring up the ongoing stand-off in eastern Ukraine, where Moscow stands accused of supporting pro-Russian separatist rebels, Toner said.
Russia will use the opportunity to protest the economic sanctions imposed on its economy by the United States and its allies after it annexed Ukraine's Crimea region.
Before seeing Putin, Kerry will meet his Russian counterpart Foreign Minister Sergei Lavrov, with whom he is in regular telephone contact over the Syrian peace process.
The United States and Russia are the key sponsors of the international bid to mediate an end to the Syrian civil war through the International Syrian Support Group.
This 17-nation contact group had been planning to meet in New York under United Nations auspices on December 18 to push forward plans for a negotiated ceasefire.
The rebels met yesterday in Saudi Arabia and announced the composition of their team to open negotiations with Assad's government.
But they also insisted that Assad must step down immediately at the start of the political transition process, which has a January 1 target date.
This insistence may be a sticking point for Assad's allies in Moscow, and Kerry confirmed today he was working with the Saudis to iron out some problems with the rebel plan.
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