"Shame on you!" chanted about 3,000 people in Prague's Wenceslas Square, targeting both Zeman and populist Prime Minister Andrej Babis, his ally.
"No to attacks on Czech Television and journalists," read one banner.
The pro-Russian Zeman, who won a second five-year term in a January election, is known for his aversion to journalists.
Last May, he told his political ally Russian President Vladimir Putin that "journalists should be liquidated".
In his inauguration speech last week, Zeman accused Czech Television and some printed media outlets of "trying to manipulate the public".
The billionaire Prime Minister Babis once called Czech Television reporters "a corrupt bunch".
"Media freedom is absolutely essential," Frantisek Laudat, former right-wing lawmaker and now a National Museum employee, told AFP.
"We have seen attacks on Czech Television in the past... if the current politicians swap its management, people in this country will no longer learn what is true and we're back in the Communist times when lying was a standard," he added.
Media freedom became a sensitive issue in the region last month when Slovak investigative journalist Jan Kuciak was murdered together with his fiancee.
Kuciak was working on an article unveiling links between the Italian mafia and the Slovak government. Local police said his work was a likely motive for the murder.
"I feel anxious. I have children who are rather active so I'm worried," pensioner Alena Hrdinova told AFP at the Prague rally.
The Czech Republic and Slovakia formed Czechoslovakia until their split in 1993, four years after the country shed its totalitarian Communist rule of four decades.
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