And though the US -backed Syrian Democratic Forces (SDF), led by Kurdish militias and its multi-ethnic allies, declared victory over IS fighters after a final round of battles, the city itself has been "comprehensively wrecked".
The SDF took the National Hospital after fierce fighting overnight and early on Tuesday, said spokesman Mostafa Bali.
Clearing operations were now under way to uncover any jihadist sleeper cells and remove landmines, he added. In a briefing to reporters in Washington, a USA military spokesman, Col. Ryan Dillon, called it "momentous".
The SDF was formed by the Kurdish Popular Protection Units (YPG) militia two years ago along with a number of smaller, Arab factions.
Syrian government officials have spoken on several occasions about their determination to regain control over all of the territory they lost to the rebellion against President Bashar al-Assad, including the area controlled by the Kurds.
The SDF, backed by the US-led worldwide alliance, have been fighting IS inside Raqqa since June.
Its capture leaves the group with little more than a "dwarf territory" in neighbouring Deir Ezzor province, said Nicholas Heras, a fellow at the Centre for a New American Security think tank. They slowly encircled the city before breaking through IS defences on the outskirts in June.
Fighters hauled down the black flag of Daesh, the last still flying over the city, from the National Hospital near the stadium. Another witness said that militia fighters were celebrating in the streets of Raqqa. "22 foreign mercenaries were killed", the SDF said.
Up to 300 militants were thought to be holding out on Sunday, after Syrian jihadists and their families were evacuated along with 3500 civilians under a deal negotiated by the Raqqa Civil Council and local Arab tribal elders.
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Three years after Raqqa's capture, the Islamic State's fortunes have changed drastically.
Mr Sello said an official statement declaring victory in the city would be made soon.
Earlier, SDF spokesman Talal Sello confirmed to Efe that the militia had complete control of Raqqa but could not confirm the end of IS presence there. During that same month, a United Nations investigator warned that USA coalition bombings were causing "staggering loss of life" in Raqqa and elsewhere in Syria.
The Britain-based Syrian Observatory for Human Rights reported earlier that government forces captured all areas between the eastern city of Deir el-Zour and the town of Mayadeen to the south. Hundreds more were missing and might be buried under destroyed buildings, it said.
An worldwide charity group says tens of thousands of people who fled the northern Syrian city of Raqqa are in bad need of aid and that the "camps are bursting at the seams". It is unclear whether the US military has plans to compete with them there to take on the Islamic State, or whether the Kurdish-led SDF will be willing to extend its reach that far.
IS militants also used civilians as human shields and shot those trying to flee.
As Roy Gutman's headline for The Daily Beast read eaerlier this year, "The U.S. Is Destroying Raqqa in Order to Save It, and Civilians Be Damned".
However, the SDF and Syrian government forces - which are backed by Russian air strikes and fighters from Lebanon's Hezbollah movement - have launched separate offensives in the province with the aim of taking control of a key crossing on the border with Iraq.