There are 2,000 American troops in Syria.
The decision sent shockwaves through the White House, causing Defense Secretary James Mattis to resign in protest.
Over recent weeks, senior USA officials have offered confusing and contradictory accounts of the terms and speed with which the U.S. is leaving. While he didn't release details, a USA military official recently said equipment is being removed from the region.
But Bolton said Friday during a radio interview that talks are ongoing between the USA military and Turkey regarding the Kurdish forces that have battled IS. Also, U.S. troops are among 200 to 300 coalition troops at a garrison in southern Syria known as al-Tanf, where they train and accompany local Syrian opposition forces on patrols to counter the IS group.
In addition, USA warplanes from the aircraft carrier Stennis, patrolling the Persian Gulf, were flying missions over Syria and Iraq, Stars & Stripes reported from aboard the Stennis.
While the USA military pullout is now officially underway it has made a slow start.
The distinctive feature of the US military campaign in Syria is its partnership with the Kurds and Arabs who were willing to act as American proxies by fighting the Islamic State group without USA troops having to take the lead combat role. Following the announcement, he was forced to reiterate the U.S.'s commitment to its more substantial troop to neighboring Iraq, where the USA -led coalition is also fighting ISIS.
A US official told ABC News that in recent days military equipment has been moved out of Syria into Iraq.
The fate of USA troops in Syria was further muddled Tuesday when Turkish President Recep Erdogan said Bolton made a "grave mistake" when he demanded Turkey pledge protection of the American supported Kurdish fighters.
"Even when there was no such decision [by Trump], our President said we are going to enter the region east of the Euphrates", Turkey's Foreign Minister Mevlut Cavusoglu told privately-owned NTV.
National Security Advisor John Bolton and Secretary of State Mike Pompeo have both visited countries in the region to explain the shift in US policy.
But the Baghdad-based official did not give details and it is unclear how many vehicles or troop units had been withdrawn.
Turkey views the US-backed YPG Syrian Kurdish militia as an extension of the Kurdistan Workers' Party (PKK), which has waged a 34-year insurgency in Turkey for Kurdish political and cultural rights, mostly in southeastern areas near Syria. But the peace and stability of areas USA forces withdraw from "must be guaranteed", she added.
On Friday, U.S. national security adviser John Bolton said those talks will continue into next week.
"When the time and place comes, the terrorists here will also be buried in the ditches and trenches they have dug", he said.
Secretary of State Mike Pompeo pushed back on reports the administration was contradicting itself Thursday on a trip to Cairo, Egypt, saying "there's no contradiction whatsoever".
When Trump ordered the USA pullout on December 19, he declared victory over ISIS and said, "Our boys, our young women, our men, they're all coming back, and they're coming back now".