Journalist Al-Hosseini Abu Deif died of his injuries on Wednesday following a week-long coma.
Abu Deif received a shotgun shell to the skull as he covered clashes outside Ithadiya Presidential Palace last week.
A funeral was held on Wednesday afternoon from Al-Qasr Al-Aini hospital through to the headquarters of the press syndicate and finally to Omar Makram Mosque in Tahrir Square.
Forensics specialists from Zeinhom morgue made their way to the hospital to conduct an official autopsy.
Abu Deif was a reporter for Al-Fajr newspaper as well as being an independent video journalist.
He was shot down as he filmed last week’s clashes between supporters of President Mohamed Morsy and opposition demonstrators outside the Presidential Palace.
His friends claimed on Sunday that he was “assassinated” by the Muslim Brotherhood for documenting the groups’ assaults on protesters during the clashes.