Mr Kerry declared the two countries can make a significant difference in the fight against IS in Syria.
It comes as Saudi Arabian officials announce a newly formed 34-state Islamic military coalition to combat terrorism.
An at-times frosty relationship between the United States and Russia appears to have warmed as 2015 draws to a close.
There was a wide smile on Vladimir Putin's face as he greeted the US Secretary of State.
John Kerry is in Russia attempting to find common ground on the Syrian crisis.
Both countries are carrying out bombing raids in the war-torn country but are at odds over the best strategy.
Russia insists it is targeting I-S, but coalition forces say many of its raids appear to be on non-IS anti-Assad opposition and militant groups.
Russia, meanwhile, accuses the US of dividing militants into "good" and "bad" groups.
There have been no accusations from either side today.
Instead there was a vote of confidence from Mr Kerry that an agreement will be reached.
"There is absolutely no question that when the United States and Russia work together effectively, our two countries benefit, and we think also so does the global community. So despite our countries' differences we've demonstrated that when the United States and Russia pull together in the same direction, progress can be made."
Mr Kerry also met Russian foreign minister Sergei Lavrov for talks, and described the meeting as "good".
The Moscow meetings are in preparation for a third round of talks among world powers on Syria, scheduled for Friday at the United Nations headquarters in New York.
President Putin says he also wants to find a way to end the conflict.
"Well you know that together, we are looking for ways out of the most urgent crisis. I know that after our meeting in Paris, the American side prepared its proposals with regard to the settlement of a number of crises, including the Syrian one."
A key player in the coalition against IS, Saudi Arabia, says it is also acting decisively against jihadist groups.
It has announced a 34-state Islamic coalition to combat not only IS, but what it's calling "all terrorism" in the region.
Included in the alliance are Egypt, Qatar, the United Arab Emirates, Malaysia, Pakistan, Turkey and some African states.
Saudi Arabia's Defence Minister Mohammed bin Salman says it will coordinate efforts to fight terrorism.
"Today there are a number of countries that suffer from terrorism, for example Daesh in Syria and Iraq; terrorism in Sinai, terrorism in Yemen, terrorism in Libya, terrorism in Mali, terrorism in Nigeria, terrorism in Pakistan, terrorism in Afghanistan and this requires a very strong effort to fight. Without a doubt, there will be coordination in these efforts."
Saudi Foreign Minister Adel Al-Jubeir explained the coalition will share information and train, equip and provide forces if necessary.
"There also has to be a military component to this because you have to deal with the terrorists at three levels: the men, the money and the mindset. The men, in terms of combat and in terms of military force, the money in terms of removing or stopping the flow of funds and choking the funds off from the terrorists, and the third component is the mindset, confronting the ideology of extremism and the ideology that promotes the killing of the innocent, which is contrary to every religion, and in particular the Islamic faith."
A notable absentee from the alliance is Iran, considered to be Saudi Arabia's arch-rival for influence in the Arab world.
The turmoil in Yemen, which has pitted Saudi fighters against Iranian-backed Houthi rebels, is seen by many as the decisive factor behind the snub.
The United Nations says a seven-day ceasefire is now in effect in Yemen between government forces and the Houthis.
The truce coincides with the start of UN sponsored peace talks in Switzerland, aimed at clinching a permanent ceasefire and a political transition.
But residents in the Yemeni capital, Sanaa, have mixed expectations.
"Out of optimism, we hope for positive results. But the general atmosphere suggests that it's useless, even if an initial agreement is put down on paper, we need ten years or more to restore the social fabric to its normal state."
