Protestors also marched through the capital, holding banners saying, "Stop the new arms race" and chanting slogans like "No radar base here."
They also presented a letter intended for President Barack Obama to the U.S. embassy.
Vojtech Filip, chairman of the Czech Communist Party, which organized the protest, said his party wants a referendum on stationing a radar base near Prague.
Other groups including the Mayors' League Against Radar also took part in the rally.