Sharoon Masih from the Vehari District in the Punjab is said to have suffered years of institutional peer bullying and discrimination because of his faith.
Coming from a poor background, his parents saved up to pay for his education at MC Model Boys Government High School Burewala and District Vehari.
The only Christian in his class, Sharoon was regularly called derogatory names and threatened.
He died in the classroom after reportedly being attacked by a mob.
The school's head teacher has since been dismissed, and the prime suspect has been arrested.
Speaking to the British Paskistani Christian Association (BPCA), his mother Razia Bibi, said: "My son was a kind-hearted, hard-working and affable boy. He has always been loved by teachers and pupils alike and shared great sorrow that he was being targeted by students at his new school because of his faith.
"Sharoon and I cried every night as he described the daily torture he was subjected to. He only told me about the abuse and violence he was facing. He did not want to upset his father because he had such a caring heart for others."
The BPCA is now offering financial assistance to Sharoon's family.
Chairman Wilson Chowdhry said: "Christians are despised and detested in Pakistan they are a constant target for persecution.
"This killing of a young Christian teenager at school, serves only to remind us that hatred towards non-Muslims is bred into the majority population at a young age, through cultural norms and a biased national curriculum.
"This young family will have to cope with the immense emotional pain of a totally avoidable incident. It is a poor indictment of MC Model Boys Government High School that a Christian could be targeted in this fashion.
"However by no means is such treatment an anomaly - it is an expectation that Christians will face abuse and violence during the years in the educational system."