Retired NATO general and former Czech army chief Petr Pavel, a pro-Western candidate who backs aid for Ukraine, beat former prime minister and billionaire Andrej Babis, one of the country's richest men, according to interim results.
Pavel, a former paratrooper, won 57% of votes while Babis scored 42%, with over 95% of the vote counted, according to the Czech Statistical Office.
Turnout in the EU and NATO member country of 10.5 million people was unusually high at 70% following an acrimonious campaign marked by controversy, death threats and a brazen hoax.
The 61-year-old Pavel will replace President Milos Zeman, an outspoken and divisive politician who fostered close ties with Moscow before making a U-turn when Russia invaded Ukraine last year.
Voting in the run-off started on Friday and is due to end on Saturday. Results are expected within hours of the polls closing.
Pavel, a 61-year-old retired general with a white beard, campaigned as an independent and has the backing of the center-right government that ousted Babis from power in a 2021 parliamentary election.
Babis, 68, a combative business magnate who had been prime minister since 2017, has sought to attract voters struggling with soaring prices and has vowed to push the government to do more to help them.
Betting agencies say Pavel is 10 times more likely to win than Babis, and he led final opinion polls by double-digit margins.
Pavel said on Friday after casting his ballot that his motto was decency and cooperation.
"(I would be) a president who will hold office with dignity," he said, and someone who "will not paint castles in the sky, but will describe reality as it is."
Czech presidents do not have many day-to-day duties but they pick prime ministers and central bank heads, have a say in foreign policy, are powerful opinion makers and can push the government on policies.
Pavel has backed keeping the central European country of 10.5 million firmly in the European Union and NATO military alliance and supports the government's continued aid to Ukraine since Russia invaded it last year.
"I believe it will be important to continue to explain to people why it is important to support Ukraine," he said on Friday.
He favors adopting the euro, a long-dormant topic under numerous governments, and progressive policies such as gay marriage.
A career soldier, Pavel joined the army in Communist times, was decorated with a French military cross for valor during peacekeeping in former Yugoslavia in the 1990s, and later rose to lead the Czech general staff and become chairman of NATO's military committee for three years before retiring in 2018.
Babis heads the biggest opposition party in parliament and has attacked Pavel for being the government's candidate since the two emerged from the first round of the election with around 35% of the vote each.
He has labeled the election as a referendum on himself, saying people should support him if they felt "worse off" now than under his former government. "I would be their voice," he said on Friday.
He campaigned on fears of the war in Ukraine spreading, and sought to offer to broker peace talks. He also suggested that as a former soldier, Pavel could drag the Czechs into a war, a claim Pavel has rejected as warmongering.
Babis also has the support of outgoing President Milos Zeman, a divisive figure over his 10 years in office who pushed for closer ties with Beijing and – until Russia invaded Ukraine – Moscow, as well as fringe forces including the pro-Russian Communist Party.