The leader has been identified as Abu Hussein al-Qurayshi.
Erdogan told broadcaster TRT Turk the IS leader was "neutralised" in a Turkish MIT intelligence agency operation on Saturday, reports BBC.
The ISIS terror group did not comment on the issue so far.
The MIT intelligence agency had been following Qurayshi for a "long time", Erdogan was quoted as saying by BBC.
"We will continue our struggle with terrorist organisations without any discrimination," he added, providing no further details.