David vs Goliath
"We are fighting a David and Goliath battle," said Jan Tamas, one of the demonstration's organisers.
"After a year we can see that the government ignores public opinion and all arguments against the base. We must call for their dismissal," he said, prompting chants of "dismiss, dismiss", from the crowd.
"No American base in the Czech Republic", "We do not want US occupiers and their radar", read some of the banners at the protest.
Several hundred people from the towns and villages nearby were bussed into Prague to take part in the protest, organisers said.
Police said the total number of people at the protest was closer to 1,000.
On Saturday, Topolanek repeated his support for the radar which, together with 10 interceptor missiles in neighbouring Poland, is aimed at defending against rocket attacks from so-called "rogue" states.
Topolanek has argued that the base forms a pert of the country's development following the withdrawl of the last Russian troops in the country in 1991.
"We should be active elements in political security," he said at a news conference following a meeting of party leaders.
But polls have shown around two-thirds of Czech opposed the US base.