Shaheer Khan sustained severe burn injuries in the horrific incident in the Orangi Town area on September 14 and was rushed to the hospital, wher he succumbed to his injuries two days later, Daily Mail reported.
His father, Nazir Khan, reportedly poured kerosene over Shaheer and lit a match in an attempt to terrify the boy into completing his homework, but the flame ignited the oil and set the child ablaze, the report said.
Hearing her boy's manic screams, Shaheer's mother Shazia dashed into the room where both parents threw blankets and clothes on the burning child in a desperate attempt to extinguish the flames, but their efforts were not enough to save him.
Upon receiving the news of her son's intolerably painful death on September 16, Shazia took two days to grieve the loss before choosing to file a case against her husband, Daily Mail reported.
The police arrested Nazir the next day and he will remain in custody until a court hearing on September 24.
Local police officer Salim Khan told Pakistani news outlets that Nazir became enraged when Shaheer insisted on going out to fly a kite instead of completing his homework.
Nazir demanded that Shaheer answer a series of questions about his work, to which the 12-year-old gave 'unsatisfactory answers'.
The father told the police he tipped the highly flammable liquid over the kid and lit a match in a bid to scare him, Daily Mail reported.
Nazir reportedly confessed to his crime upon being arrested after his wife filed a case against him.
Orangi Town in the port city of Karachi is believed to be home to close to three million people. Widely cited as one of Asia's largest slums, it sprawls over 8,000 acres - the equivalent of about 4,500 Wembley football pitches.