The accused are boys aged 13, 14 and 15 years and they also alleged that the deceased boy used to bully them in school and also while playing in the locality, said police.
The victim was reported missing on November 19 and his body was found in a decomposed state near the railway tracks close to Zakhira flyover after three days, said police.
The area where the body was found, comes under the jurisdiction of the west district of Delhi Police.
During the scuffle, two of the boys allegedly held the victim and another attacked him with a knife. When he collapsed, the trio fled the spot, police added.