President Abdel-Fattah El-Sisi and leading officials attended a state funeral procession at the Unknown Soldier Memorial in the Nasr City for the victims of a bombing which took place at the St Peter and St Paul church a day before, killing 24 people.
A funeral service was conducted by Pope Tawadros II at the Church of the Virgin Mary, also in Nasr City, on Monday morning.
Dozen of buses are taking the victims' families and the coffins of those killed to the state funeral, which will be attended by President Abdel-Fattah El-Sisi and senior state officials.
Twenty-four people were killed and 49 injured after a bomb exploded inside the church attached to the Coptic cathedral in Cairo on Sunday, one of the deadliest attacks on Egyptian Christians in years. Twenty-three died on Sunday; a twenty-fourth casualty died early on Monday morning, according to the health ministry.
"This calamity is not against the church but against the homeland, [against] all of Egypt," Pope Tawadros said after the funeral service.
"We are in a lot pain because of this evil.. but we are pleased they passed away during prayers, this is the best time to die.. during this [holy] month."
Pope Tawadros, who cut short a visit to Greece to return to Cairo after the attack on Sunday, said that the Greek president and the head of the Greek church send their condolences to Egypt.
"Whoever did this attack does not belong to the Egyptian people," the cleric said.
The church service was attended by relatives only, according to a statement from the church.
Mourners who were not allowed inside the church prayed outside behind a security cordon.
Following the attack, President El-Sisi announced that the country will observe three days of mourning.
A number of countries including Russia, US, Germany and Saudi Arabia, have condemned the bomb attack.