The village of Trokavec organised the vote to show the strength of the villagers' opposition to the project, part of a US-proposed missile defence shield, which Czech and US officials are currently discussing.
But the vote was symbolic and holds no legal power.
The result of the informal vote reflects growing opposition in the Czech Republic to the planned missile shield.
Recent polls have show that nearly two-thirds of Czechs oppose the plan, which the US says is needed to defend against possible missile attacks by "rogue nations" such as Iran or North Korea.
Poland is also being asked to host missile batteries which form part of the system.
Meanwhile, in Prague, several hundred demonstrators gathered on Saturday evening in the city's Old Town square, many carrying torches, to protest against the Iraq war and the proposed anti-missile radar base.