Police previously said the gunman – a 24-year-old student at the Faculty of Arts at Charles University in Prague – had been “eliminated”.
His body was found in the university’s philosophy building, according to officials.
Police said the gunman’s father was also found dead earlier on Thursday.
Officers were still sweeping the area, including the building’s balconies, for possible explosives.
The mass shooting is the deadliest in the Czech Republic in recent times – the last being in 2019, when seven people were killed by a gunman who later took his own life, in the Ostrava hospital attack.
Prague Mayor Bohuslav Svoboda told Czech television: “We always thought that this was a thing that did not concern us.
“Now it turns out that, unfortunately, our world is also changing and the problem of the individual shooter is emerging here as well.”
The incident took place in the area of Jan Palach Square, in the city’s Old Town district.
The area is home to The Philosophical Faculty of Charles University and the Academy of Arts, Architecture, and Design.
Klara, a student at the university, told local media that she was among those who police evacuated from the building.
“It was terribly scary,” she told iDnes.cz.
“There were a lot of policemen everywhere, who were shouting at us with submachine guns, telling us to run outside.”
Prague mayor Bohuslav Svoboda said both the Philosophical Faculty of Charles University and the Academy of Arts, Architecture and Design, had been evacuated during the shooting.