BEIRUT—Clashes between members of al-Qaida’s branch in Syria and a rebel faction in the country’s north believed to have been trained by the U.S. government have stopped after the rebels left their headquarters, activists said on Saturday.

The fighting came a few days after the U.S. and Turkey announced the outlines of a deal to help rebels push Islamic State militants back from a strip of territory it controls along the Syrian-Turkish border, replacing it with more moderate rebels backed by Washington and Ankara.

Rami Abdurrahman, who heads the Britain-based Syrian Observatory for Human Rights, said members of the so-called Division 30 faction fled to a nearby area controlled by a Syrian Kurdish militia. Abu al-Hassan Marea, a Syrian activist who is currently in Turkey near the Syrian border, confirmed on Saturday that Division 30 fighters have withdrawn from their headquarters.

Messrs. Abdurrahman and Marea said Division 30 had less than 60 fighters and that on Friday alone the group lost five fighters, while 18 others were wounded.

A representative of Division 30 didn’t respond to written questions sent to the group’s Facebook account.