Arafat, a 12-year-old madrasa student who was shot by police during the anti-discrimination student movement, succumbed to injuries on Sunday night.
The minor boy was undergoing treatment at Dhaka's Combined Military Hospital.
His namaz-e-janaza was held on Monday at the Central Shaheed Minar in Dhaka.
Arafat's brother Hasan Ali led the namaz-e-Janaza.
Adviser of the Interim Government Nahid Islam, Arafat's father Shahidul Islam, Special Assistant for the Health Ministry Sayedur Rahman, Press Secretary to the Chief Adviser Shafiqul Alam, student leader Sarjis Alam, among others, attended the funeral prayer.
