In 2013 Zeman, then a former left-leaning prime minister, became president after defeating former conservative Foreign Minister Karel Schwarzenberg in the second round of the election.
As well as leading calls against accepting migrants from Muslim countries, he has focused on building ties with Beijing and Moscow, including calling for the removal of European Union sanctions on Russian Federation imposed over its annexation of Ukraine's Crimea.
Political analyst Jiri Pehe told AFP the outcome reflected the "very deep polarization" of Czech society which is "split down the middle" along rural-urban and populist-liberal lines, echoing divisions elsewhere in Europe and in the US. Zeman, seen as a Russia-friendly politician, was one of the few European leaders to endorse Donald Trump's bid for the White House. His challenger, a 68-year-old chemistry professor, vowed to "return dignity" to the post, a reference to Mr Zeman's frequent clashes with media and political rivals.
Speaking to supporters after claiming victory, Zeman said he would continue travelling the country to meet citizens and hear their worries.
The polling stations are due to reopen at 0700 GMT on Saturday before closing definitively at 1300 GMT. The victor of the vote may also influence a complicated political situation after billionaire Premier Andrej Babis's minority administration was forced to resign when it failed to win approval from lawmakers earlier this month.
He has promised to give Prime Minister Andrej Babis, a billionaire businessman, a second chance to form a government after his minority cabinet lost a confidence vote in parliament last week.
Zeman has also won support from the far-left Communist party and the far-right, anti-EU and anti-Nato SPD party.
A poll by the Kantar TNS and Median agencies showed Zeman scoring 45.5 percent of the vote against 45 percent for Drahos. "Today my opponent was not dealing with politics until this point", Zeman said.
Zeman has benefited from, and reinforced, Czech hostility to immigration from Muslim countries, although the country was not the target of any significant number of refugees.
His opponent, former Czech Academy of Sciences head Jiri Drahos, whose views are closer to the European mainstream, garnered 48.6 per cent.
Zeman voted Friday under heavy security in Prague. 'If I had to pick based on likeability, I would vote Drahos; he looks good and carries himself well.
Both Zeman and Drahoš have rejected the EU's refugee quotas, but unlike Zeman, Drahoš has said his country should differentiate between economic migrants and war refugees and follow the bloc's asylum procedures.
Drahos also said he saw Russian Federation as a security threat because Moscow sees North Atlantic Treaty Organisation as its adversary.