In neighbouring Deir Ezzor province meanwhile, Syria's army captured the ISIS stronghold of Mayadeen, in the latest blow to the jihadists who are seeing their self-styled "caliphate" crumble.
A war monitor said no Syrian members of the jihadist group remained in Raqa and that negotiations on the fate of foreign fighters were ongoing.
But the US-led coalition backing the offensive insisted that foreign fighters would not be allowed to leave the city.
Raqa was once the de facto Syrian capital of the jihadist group's "caliphate" and the city's loss would be a new blow for ISIS, which has already been driven from its strongholds in Iraq, including second city Mosul.
In June, the US-backed Syrian Democratic Forces (SDF), an alliance of Kurdish and Arab fighters, broke into Raqa, and since then they have captured around 90 percent of the city.
In recent days, talks had been under way on a deal to secure the last parts of Raqa while protecting trapped civilians, some of them being used by ISIS fighters as human shields.
On Saturday, the US-led coalition confirmed dozens of ISIS fighters had handed themselves in.
"Within the past 24 hours, approximately 100 ISIS terrorists have surrendered in Raqa, and were removed from the city," the coalition said in a statement.
Earlier, the Syrian Observatory for Human Rights, a Britain-based monitor of the war, reported that all the remaining Syrian ISIS members in the city had now left with their families.
"All Syrian fighters from the Islamic State group left Raqa over the past five days," said Observatory head Rami Abdel Rahman. They numbered around 200 fighters.
Members of the RCC - a provisional administration for the city, set up by the SDF - had been working with tribal leaders throughout the week to try to secure safe passage for civilians.
Up to 1 500 civilians have managed to flee the battle-ravaged city in the past week, according to the coalition. The United Nations estimates thousands more may still be trapped inside.