He won 55% of votes in the second-round poll, compared to Foreign Minister Karel Schwarzenberg's 45%.
Mr Zeman won 24.2% in the first round poll, with Mr Schwarzenberg winning 23.4%.
He defeated Karel Schwarzenberg, an aristocratic foreign minister with the TOP09 party, who garnered 45.2%.
Karel Schwarzenberg, an aristocratic former foreign minister with the TOP09 party, was in second place with 45.1%.
Other candidates include Foreign Minister Karel Schwarzenberg, current and former senators and MEPs as well as two artists.
The EU delegation, led by Czech Foreign Minister Karel Schwarzenberg, also aims to facilitate humanitarian aid for Gaza residents.
Former Czech Prime Minister Milos Zeman is set to face Foreign Minister Karel Schwarzenberg in a run-off in the Czech Republic's presidential election.
"There was nobody very hot about this, that's perfectly true, " Czech Foreign Minister Karel Schwarzenberg, whose country holds the EU Presidency, conceded after Monday's meeting.
Schwarzenberg was personally and professionally close to late President Vaclav Havel.
With almost all the votes counted in the first round of voting, Mr Zeman has emerged as the front runner, with Mr Schwarzenberg in second place.
The urban elite voted en masse for Mr Schwarzenberg - who was supported by many in the media and had a strong Facebook following, says our correspondent.
Former prime minister Milos Zeman won the first direct Czech presidential election in January 2013, beating conservative Foreign Minister Karel Schwarzenberg by a margin of 55% to 45%.
Karel Schwarzenberg is a titled prince, 75 years of age but wildly popularly amongst young, urban voters - and closely linked to the country's first president, the late Vaclav Havel, he adds.
On February 10, in an appearance with Czech Foreign Minister Karel Schwarzenberg, Clinton signaled that the United States might rethink plans for a missile defense shield in Europe if Iran decides against pursuing nuclear weapons.
CNN: Obama downplays letter to Russia regarding nuclear Iran
Although Czechs are generally disillusioned with politics, they turned out in their droves to choose between the two very different candidates - Mr Zeman, the acerbic former Social Democrat prime minister, and Karel Schwarzenberg, the elderly, aristocratic foreign minister.
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