Activists say about 35 pro-government fighters were killed and some medical staff taken hostage. More than 20 ISIS fighters were also reported killed.
The attack was centered on al-Assad hospital, to the west of the city.
Syrian government forces retook the hospital after several hours, reports say, but the fate of the hostages is unclear.
ISIS controls more than of half of Deir al-Zour and is seeking to capture the entire city.
The jihadist group has been besieging government-held areas there for two years, trapping about 200,000 civilians.
ISIS’s Amaq news agency said its fighters had carried out a “major offensive” in Deir al-Zour on May 14, storming the hospital and cutting the route between a Syrian army base and the city’s airport.
Amaq said it had also taken over a fire station, university accommodation, grain silos and territory near the al-Tayyam oil fields.
According to the Syrian Observatory for Human Rights, government forces retook the hospital after several hours of fierce fighting.
Deir al-Zour is in an oil-rich area and on a vital supply route to the ISIS stronghold of Raqqa.
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