Thousands of people carried football-style red cards as a warning to Milos Zeman, while others threw eggs. One accidentally hit the German president.
Many are angry with Milos Zeman, who they see as too sympathetic to Russia.
The Velvet Revolution began on November 17, 1989, when police attacked a student protest.
A wave of demonstrations followed across the now Czech Republic, toppling the communist government and replacing it with one led by dissident playwright Vaclav Havel.
Some Czechs feel that certain aims of the revolution, such as the promotion of human rights, have been sidelined by Milos Zeman.
They also worry that the president, a former communist, is too close to both Russia and China.
On November 17, demonstrators carried banners reading “down with Zeman” and “we do not want to be a Russian colony”.
As the president unveiled a plaque to the students involved in the 1989 protest, he was booed, jeered and pelted with eggs.
Though Milos Zeman appears not to have been hit, German President Joachim Gauck was struck during the attack.
Milos Zeman angered many Czech citizens when he defended Russia’s stance on Ukraine, declaring the conflict there “a civil war between two groups of Ukrainian citizens”.
Though Moscow has long denied any direct involvement in the Ukraine crisis, the EU, of which the Czech Republic is a member, has imposed sanctions on Russia, saying it has supplied separatist rebels there with weapons and Russian fighters.
The Czech president also used derogatory language when discussing Russian protest group Pussy Riot in an interview earlier this month.
In October Milos Zeman shocked some when he said he wished to learned how China “stabilized” its society.
In the run-up to Monday’s celebrations, Milos Zeman said the 1989 student protest had not triggered the Velvet Revolution.
Despite his participation in it, Milos Zeman said the historic protest had been just one of “any number of rallies” and he played down police brutality.
Milos Zeman still has the backing of many voters and his supporters were scheduled to hold a rally on November 17.
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