State media quoted a security official blaming "criminal elements" for the unrest, which broke out after nearly a month of protests across Iran over the death in detention of Mahsa Amini, a 22-year-old Kurdish Iranian.
The official said calm had returned, but one witness said gunfire could still be heard.
"Roads leading to Evin prison have been closed to traffic. There are lots of ambulances here," said a witness contacted by Reuters. "Still we can hear gunshots."
Another witness said families of prisoners had gathered in front of the main prison entrance. "I can see fire and smoke. Lots of special forces. Ambulances are here too," they said.
The activist website 1500tasvir shared video footage it said showed special forces on motorbikes heading for the prison.
The prison mostly holds detainees facing security charges, including Iranians with dual nationality. It has long been criticised by Western rights groups and it was blacklisted by the US government in 2018 for "serious human rights abuses".
Siamak Namazi, an Iranian American imprisoned for nearly seven years on espionage-related charges rejected by Washington as baseless, returned to Evin on Wednesday after being granted a brief furlough, his lawyer said.
Human Rights Watch has accused authorities at the prison of using threats of torture and of indefinite imprisonment, as well as lengthy interrogations and denial of medical care for detainees.
The unrest at Evin prison came after nearly a month of protests across Iran since Amini - a 22-year-old woman from the country's Kurdish region - died on September 16 while being held for "inappropriate attire".
The protests have posed one of the most serious challenges to the Islamic Republic since the 1979 revolution.
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