"Our activities continue for the protection of our national security, to prevent any undesirable entity, to allow our displaced Syrian brothers and sisters to return to their country, and to ensure security and stability in the region," the military said.
The Turkish armed forces said in a statement this "phase" of its operation against IS and "terrorists" in the region was "successfully completed".
The completion of the operation dubbed "Euphrates Shield" had been announced by Prime Minister Binali Yildirim on Wednesday, who nevertheless did not rule out new military campaigns inside Syria.
At the time, neither Yildirim nor the top advisory national security council had said whether or not there were plans to withdraw Turkish troops.
Turkey launched in August its unilateral operation with Syrian rebels to remove IS from its border and to halt the Kurdish militia advance.
Dozens of Turkish soldiers were killed by IS during clashes and attacks as Turkey-backed Syrian opposition fighters recaptured towns including Jarabulus, Al-Rai, Dabiq and Al-Bab.
President Recep Tayyip Erdogan's spokesman Ibrahim Kalin said Friday the completion of the military operation did not mean Turkey would ignore what takes place on its southern border.
"There should be no meaning taken from this that Turkey will remain indifferent to the security risks or will not engage there," Kalin told reporters in Ankara.
"Just the opposite actually, security measures in the region continue at the highest level," he added, without giving further details.
Turkey has suggested it wants to join any operation to capture IS stronghold Raqa, but without the Kurdish militia it views as terrorists.
Turkey appears to be sidelined as US-backed Syrian Democratic Forces including Kurdish fighters are laying the groundwork for an assault on the heart of the jihadists' so-called caliphate.
US Secretary of State Rex Tillerson would give no comment on Turkish involvement during his visit to Ankara on Thursday.