Ebrahim Raisi and seven other people died in a crash near the country’s border with Azerbaijan on Sunday.
Ayatollah Ali Khamenei, the Supreme Leader, delivered prayers for the victims during the funeral at Tehran University.
The caskets of the deceased, including the late foreign minister Hossein Amirabdollahian, were covered in Iranian flags with their photographs on them.
A black turban adorned the late president’s coffin, representing him as a direct descendant of Islam’s Prophet Muhammad.
“Oh Allah, we didn’t see anything but good from him,” Mr Khamenei said during the traditional Arabic prayer for the dead.