The two heads of state will sign a successor to the 1991 Strategic Arms Reduction Treaty (Start), which expired last December, in the city where Obama called for a nuclear-free world in a keynote speech a year ago.
The deal aims to reduce the number of deployed warheads by 30 per cent from the levels set in the last major US-Russian disarmament treaty in 2002, specifying limits of 1,550 nuclear warheads for each of the two countries.
Richard Weitz, the director of the Hudson Institute's Center for Political-Military Analysis, told Al Jazeera the treaty, in terms of nuclear cuts, is not so substantive.
"In terms of the reductions themselves, the treaty is not so substantive, it is, however, a modest confidence boosting measure.
"The limits are somewhat lower than in previous treaties. But if we hadn't reached this treaty people would become very concerned," he said.
"That which will happen in Prague tomorrow will be a very important step in the process of disarmament and non-proliferation of weapons of mass destruction," Medvedev said.
He arrived in Prague from Bratislava, the capital of neighbouring Slovakia, where he commemorated the 65th anniversary of the city's World War II liberation.
He is scheduled to meet Obama and Klaus before the signature and leave for Moscow after a joint ceremonial lunch on Thursday afternoon.
Obama will meet 11 European leaders on Thursday evening, spend the night in Prague and leave around noon (10:00 GMT) on Friday after bilateral talks with Czech leaders.