Results from 94.95 percent of voting districts showed Zeman led the run-off election round with 52.16 percent of the vote to 47.83 percent for his opponent Jiri Drahos.
It means the 73-year-old looks to have secured a second term in charge of the nation, beating pro-EU academi Drahos.
And he did it on the back of a tough stance against immigration and courtship of closer ties with Russia and China.
Mr Zeman has also caused panic in Brussels by failing to rule out his own Brexit-style referendum.
During a TV debate, Mr Zeman said Czech citizens should have a direct say on political issues and that he is not opposed to a referendum on EU membership.
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He said: “Brexit is a decision that must be respected.”
Mr Zeman declared he was for the adoption of the common currency, in principle, but he did not want to allow “Czech taxpayers to pay Greek debt”.
He said: ”The moment Greece leaves the eurozone or is excluded, I will gladly support it.”
More to follow.