Zeman has no power to call a referendum, which would require a constitutional amendment. But he is an influential leader in a country where many voters are sceptical about the EU, which the Czech Republic joined in 2004.
"I disagree with those who are for leaving the European Union," Czech Radio quoted Zeman as saying at a meeting with citizens in the eastern Czech town of Velke Mezirici on Thursday evening.
"But I will do everything for them to have a referendum and be able to express themselves. And the same goes for a NATO exit too," the centre-left president added.
The UK voted to leave the EU by 52% on June 23 referendum.