The treaty limits both sides to 1,550 warheads, about 30% less than currently allowed, the White House said.
The deal replaces the 1991 Strategic Arms Reduction Treaty. It will be signed in Prague on 8 April.
Both sides agreed to cut their arsenals last year, but disagreements on verification have held up a deal.
In a speech in Prague last year Mr Obama set out his vision of moving towards a world without nuclear weapons.
Moral high ground
The US is said to have more than 2,000 deployed strategic nuclear weapons, while Russia is believed to have more than 2,500.
The new agreement - which came in a phone call between the two leaders - limits the US and Russia to a maximum of 1,550 deployed nuclear warheads each. Both sides will also reduce the number of missiles that carry the warheads.
The cuts are substantial - well over 30% for the Russians and around 25% for the Americans, whose current arsenal is smaller, says BBC diplomatic correspondent James Robbins.
The timing and symbolism are crucial, enabling both countries to claim some moral high ground going into next month's Washington Summit on nuclear security, and the critical talks in May aimed at limiting the spread of nuclear weapons around the world, our correspondent says.
Presidents Obama and Medvedev hope the new deal will increase pressure on Iran, in particular, to abandon any ambition to develop nuclear weapons, he adds.
"This landmark agreement advances the security of both nations, and reaffirms American and Russian leadership on behalf of nuclear security and global non-proliferation," the White House said in a statement.
The agreement - called the Measures to Further Reduction and Limitation of Strategic Offensive Arms - replaces the Cold War-era Start treaty signed in 1991 and the Moscow Treaty signed in 2002.
It furthers Mr Obama's commitment to "reset" relations with Moscow, the statement added.
The treaty must be ratified by the US Senate and the Russian Duma.
BBC
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