And while about 2,000 American troops are now based in the civil war-torn country, that number could increase before a final pull-out, according to the New York Times.
The US president also warned that it "will devastate Turkey economically if they hit Kurds".
But, he added, "we also know that those are fighting alongside of us for all this time deserve to be protected as well".
He said: "Terrorists can't be your partners and allies".
No U.S. personnel have left Syria yet, according to a Pentagon spokesman.
More than 2,000 USA troops are serving in Syria.
Trump's decision to leave Syria, which he initially said would be rapid but later slowed down, shocked US allies and angered the Kurds in Syria, who are vulnerable to attack by Turkey. "They understand that there are squabbles in Washington, but their mission remains, their duties continue and they're executing them".
More than 600 people, mainly women and children, were evacuated on 25 buses sent by the Syrian Democratic Forces (SDF), the Britain-based Syrian Observatory for Human Rights said. Previously Washington said that it would not disclose a timeline for the withdrawal of its troops, and pledging that the US-led worldwide coalition's fight against terrorism would continue.
US Secretary of State Mike Pompeo has said he is confident that the Trump administration and Turkey can agree a way to protect the Kurdish fighters in Syria after US troops leave the country.
The bilateral relations have been further aggravated by USA threats to halt the transfer of military tech to its North Atlantic Treaty Organisation ally, including the fifth generation F-35 stealth fighter jets, and even to impose sanctions over Turkey's commitment to purchase Russian S-400 air defense systems, a diversification of weapons suppliers that enhances its national security.
Residents near border crossings that are typically used by United States forces going in and out of Syria from Iraq said they had seen no obvious or large-scale movement of USA ground forces on Friday.
Erdogan said Bolton was making a "serious mistake".
In a speech in Cairo on Thursday, Mr Pompeo vowed that the United States would "expel every last Iranian boot" from Syria, where Tehran is supporting Syrian President Bashar al-Assad.
His top diplomat Mike Pompeo is on a whirlwind regional tour aimed at reassuring Washington's Kurdish allies in the fight against Isis.
The pullout was reportedly sparked after a phone conversation between Trump and Turkish President Recep Tayyip Erdogan.
Ankara sees the YPG as a terrorist group linked to the Kurdistan Worker's Party (PKK) which has fought a decades-long insurgency against the Turkish state.