The interior ministry did not identify the suspect, but said he was a leading member of IS and "dangerous", and was killed in a National Guard operation on Sunday night near the border with Algeria.
Eleven arrest warrants had been issued for the suspect in connection with "terrorist operations", the ministry said.
Judiciary spokesman Sofiene Sliti told Shems FM radio the suspect was a Tunisian known as Houssem Tlithi, born in 1997.
The interior ministry said he had been on the run since 2014 and hiding in the Mount Salloum region, a jihadist stronghold.
During Sunday night's operation, another jihadist was wounded and weapons seized, including a Kalashnikov assault rifle and material used to make explosive belts.
The interior ministry said they were to be used for "terrorist" attacks during Ramadan, a holy month which started on Saturday and during which believers abstain from eating and drinking from dawn to dusk.
Interior ministry spokesman Yasser Mesbah said three people were arrested as part of the operation, including a man and a woman detained on Monday.
The country has been under a state of emergency since November 2015, when a suicide bombing in Tunis claimed by the Islamic State jihadist group killed 12 presidential guards.
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