The deal will allow the United States to transport personnel and equipment across Russian territory to supply U.S. and coalition forces in Afghanistan.
"This is a substantial contribution by Russia to our international effort, and it will save the United States time and resources in giving our troops the support that they need," Obama said at a news conference with Medvedev.
In a written statement, the White House said the deal "complements a NATO-Russia arrangement, under which the United States began shipping non-lethal equipment to Afghanistan through Russian territory earlier this year."
The new transit routes will allow the U.S. military to resupply international forces more quickly, saving up to $133 million a year in fuel and other transportation costs, the White House said.
Obama and Medvedev also issued a joint statement saying they are concerned about the continuing conflict in Afghanistan and reaffirming their "commitment to the goals of the common fight against the threats of terrorism, armed extremism, and illegal drug trafficking" in the country.
"We shall continue and develop our cooperation in the interest of enhancing the capabilities of the government of Afghanistan to accomplish key socioeconomic objectives, to raise living standards, and to ensure the security of its people," the two presidents said.
Updated: 1:23 p.m.