The man was killed in a raid on a ninth-floor apartment on the outskirts of Ankara after he ignored warnings to surrender and opened fire on police, Ankara Governor Ercan Topaca said.
The state-run Anadolu Agency quoted Topaca as saying the man was believed to be planning a suicide attack in the city, either targeting large gatherings or to coincide with two national ceremonies in the coming weeks.
Topaca said police seized explosive materials from the apartment.
Turkey has been rocked by a series of deadly suicide bombings over the past 18 months that were carried out by IS or Kurdish militants.
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Officials banned demonstrations or large gatherings in Ankara until the end of November citing intelligence over possible attacks.
Interior Minister Suleyman Soylu told reporters that the man was spotted scouting Turkey's old parliament building as well as the mausoleum of Mustafa Kemal Ataturk, the founder of the Turkish republic, where ceremonies are scheduled to take place.
"The Daesh militant was rendered ineffective following very important tracking and intelligence work," Soylu said, using the Arabic acronym for IS. "These operations are continuing."
Separately, a woman and her child were wounded in a mortar attack by Kurdish militants today afternoon, according to a statement by the governor's office of Osmaniye province in southern Turkey. Four mortars were fired.
Earlier today, Kurdish rebels attacked a van carrying Turkish security force members with a rocket in southeast Turkey, killing two government-paid village guards and wounding two others, Anadolu reported.
Violence between the PKK and the security forces resumed last year, after the collapse of a fragile cease-fire agreement.
Earlier this month, two PKK militants suspected of planning a suicide car bombing blew themselves up on a farm outside of Ankara during a police operation to apprehend them.