Many Egyptians have voiced outrage over the disaster in the now scorched Abu Sifin church, located in the greater Cairo neighborhood of Imbaba west of the Nile River.
Grief has spread among Copts, the Middle East's largest Christian community, which makes up at least 10 million of Muslim-majority Egypt's population of 103 million.
Because the Coptic church fire happened during Sunday mass, when local families flock to the church and its daycare services, children were among the victims.
Though officials have not confirmed how many minors died, AFP correspondents at the funeral Sunday night saw several child-sized coffins.
Local media published a list from the Imbaba Hospital listing the names of 10 people killed who were aged under 16.
"My cousin's children died," video creator Moha El Harra said in a widely shared online livestream after Sunday's blaze, which was blamed on an electrical fault.
"I'm from the area. I know that the ambulance could have been there in three minutes. It took them an hour and a half.
"All we want is justice -- for the local ambulance authority, the fire services, civil defense. All of them need to be held to account."
As debate flared on social media, one Twitter user charged that the reportedly slow response time "is not just negligence, it's complicity."
Health Minister Khaled Abd el-Ghaffar had declared Sunday that "paramedics were informed of the fire at 8:57 am" and the first ambulance "arrived at the site at exactly 8:59 am".
But many challenged this, with eye-witnesses saying it took "an hour and a half" for emergency services to arrive.
"No, the ambulance did not arrive within two minutes," one local resident, Mina Masry, told AFP. "If the ambulance had come on time, they could have rescued people," he added, stressing that many lives were lost to smoke inhalation, not burns.
A statement from the public prosecutor's office confirmed that asphyxiation caused all of the 41 deaths as the corpses bore "no other visible injuries."
Slow response times of emergency services are not unusual in Egypt, where neighbourhood residents routinely improvise rescue efforts, even within the megalopolis of Cairo.
Smoke detectors and alarms and fire escapes are rare and in many areas, such as Imbaba, warrens of narrow roads make it hard for fire engines to reach disaster sites.
Baioumy, the neighbour, told AFP that firefighters were hampered by the church's location "on a very narrow street".