The health ministry said 25 people had been killed in the bombing at the Saint Peter and Saint Paul Church yesterday.
It was the deadliest attack in recent memory on the Christian minority, who make up about 10 percent of Egypt's population.
President Abdel Fattah al-Sisi, speaking at the funeral, said the attack was carried out by a suicide bomber who had been identified as 22-year-old Mahmoud Shafik Mohamed Mostafa.
Most of the victims were women, authorities have said.
The attack occurred during Sunday service at the church adjacent to Saint Mark's Cathedral, the seat of Coptic Pope Tawadros II.
There has been no claim of responsibility for the bombing, but Coptic Christians have been previously targeted in Egypt.
Wooden coffins, each bearing a cross, were covered with the country's flag and lined up at the Saint Mary and Saint Athanasius Coptic Orthodox Church in the Nasr City district today.
In the streets of Nasr City, Sisi and Tawadros led black-clad mourners behind soldiers carrying the coffins of the victims.
Troops marched to the sound of military music.
"This blow has caused us a lot of pain, but never will we let it break us," Sisi said.
Pope Tawadros II said: "We are hurting from this evil."
Yesterday's blast was the worst attack on the Coptic Christian community since a 2011 suicide bombing killed more than 20 worshippers outside a church in the coastal city of Alexandria.
Copts have faced persecution and discrimination dating back to the 30-year rule of Hosni Mubarak, who was toppled by a popular uprising in 2011.
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