Russia and the United States are sponsors of an international effort to broker a ceasefire and political talks between Bashar al-Assad's regime and Syria's armed opposition.
But their positions on Assad's eventual fate and the best tactics to employ against the jihadist Islamic State group differ starkly, threatening to stymie the process.
Kerry came to Moscow on Tuesday not even knowing whether Russia would agree that the next international meeting on the crisis should take place on Friday in New York.
And as he sat down with the Russian leader, despite broad smiles, it was still not clear whether there had been a breakthrough.
"I am very happy to have the opportunity to meet and talk with you," Putin said, sitting beside his foreign minister, Sergei Lavrov, who had met Kerry earlier in the day.
"Minister Lavrov just now informed me in detail about both your proposals as well as some issues which require additional discussions," Putin added.
Kerry said that he hoped to address the crises both in Syria and in Ukraine, where Washington accuses Moscow of backing separatist rebels and has imposed sanctions on Russia.
"You had a chance to speak to President Obama in New York and then subsequently in Paris," Kerry said, sitting across from a smiling Putin at a conference table in an ornate Kremlin salon.
"Both you and President Obama have committed themselves to trying to develop as much as possible ... an approach that can try to deal with Ukraine and deal with Syria," Kerry said.
"So I very much look forward to our discussion now and appreciate the seriousness of your commitment of time and thought about these issues," he added.
Then the press was ushered out, and the talks began in earnest.
Kerry and the UN envoy for Syria, Staffan de Mistura, want to hold the next round of Syrian peace talks on Friday in New York, but Moscow has so far refused to confirm the date.
Speaking after meeting Lavrov, Kerry declined to say whether the New York negotiations would go ahead on Friday.
"Well, I need to meet with the president," he told reporters on a stroll in central Moscow, where he was mobbed by Russians wanting to meet Washington's top diplomat.
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Washington is relying on the Kremlin to drag Russian ally Bashar al-Assad to the table for talks with his rebel opponents on ending Syria's vicious four-and-a-half-year-old civil war.
US ally Saudi Arabia is putting together the coalition that would negotiate on behalf of the rebels, with a view to first agreeing a ceasefire and then launching a political dialogue.
And looming over the effort to end the conflict is the threat posed by the Islamic State group to spread the carnage beyond Syria's borders.
Kerry hopes that if the regime and the rebels can agree a truce then they, Russia and a US-led coalition of Western and Arab allies can focus their fire on IS.
Washington and Moscow are the key powers in the process, leading talks through the 17-nation International Syria Support Group.
Kerry called Lavrov the "co-convenor" of the talks and thanked him for his efforts "to lead us up now hopefully to getting to New York and building on the progress that's been made."
But the talks are in jeopardy after Moscow took issue with last week's unprecedented rebel talks in Saudi Arabia.
- US frustration -
Moscow said Monday that Friday's talks should not take place until all parties agree on both the rebel representation and on a blacklist of organisations deemed irredeemable "terrorists."
US officials have expressed frustration that Assad is trying to set his own rules about which opponents he is prepared to talk to and which are irredeemable terrorists in his eyes.
They insist Russia has committed to a political transition to end the war, and warn that if it cannot get Assad to the table, the Kremlin's own forces will get bogged down in the fighting.
Ties have also been strained over the crisis in Ukraine, but the US side said it would not be drawn into bargaining with Russia over the sanctions it imposed over Moscow's interference there.
Russia has dispatched air and naval forces to Syria to shore up Assad's regime, while the United States and its allies are bombing Islamic State targets in the east of the country.
The US believes Assad's crackdown on protesters in March 2011 triggered a civil war that has killed 250,000 and driven recruits to IS, which profited from the chaos.
America's regional allies, led by Saudi Arabia, are even more emphatic in declaring that Assad must go, demanding he step down as soon as peace talks begin.
The opposition leaders met last week in Riyadh and began the process of deciding their negotiating team -- but also repeated their demand that Assad step down immediately.