Bekir Kaya was taken into custody as part of a "terror investigation", the official news agency Anadolu reported, saying he was accused of links to the outlawed Kurdistan Workers' Party (PKK).
Four other municipal officials in the city, which has a mixed Kurdish and Turkish population, were also detained, Anadolu said.
The targeting of city heads follows the arrest of 10 MPs from the pro-Kurdish Peoples' Democratic Party (HDP), including its co-leaders, who are being held on charges of links to the PKK.
Yesterday, mayors in the southeastern city of Siirt and the eastern city of Tunceli were detained following similar accusations of links to the PKK, Anadolu said.
And last month the two mayors of the mainly Kurdish city of Diyarbakir, Gultan Kisanak and Firat Anli, were detained and charged with belonging to the PKK.
All the mayors were elected in 2014 local elections.
With tensions flaring in Van, police used tear gas and water cannon outside the municipality to disperse dozens of protesters backing the detained mayor, an AFP photographer said.
EU and US officials have expressed concern over the arrest of opposition lawmakers as fears grow over Turkey's use of emergency laws.
In a sign of the tensions with the West, top EU lawmakers yesterday cancelled a visit to Turkey in a dispute over the format of the trip.
The crackdown comes as Ankara wages a relentless battle to crush the PKK, which has stepped up attacks since the collapse of a two-and-a-half-year ceasefire in July 2015.
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