The 16-year-old was the victim of a random attack in a park in Enfield, north London, two weeks ago.
He lost part of his lung in the attack and only recently returned home from hospital.
He had been expected to get good grades, including A stars, however pleas from his head teacher, MP and parents to the exam boards have been turned down, The Times reported.
If a pupil has not sat their final exams, boards can use discretionary powers to grant GCSE certificates in "rare and exceptional circumstances".
However The Joint Council for Qualifications (JCQ), which represents the boards AQA, OCR and Pearson Edexcel, told the newspaper that it would offer only an honorary award in the form of a letter – not the same as a certificate – that explained why he could not complete his course.
The boy’s father, an executive in a telecommunications company, is concerned that his son would carry around the stigma surrounding knife crime when he tries to get jobs in the future.
He told The Times: "People automatically assume that it's gang-related, drug-related or 'black-on-black' crime.
“In fact the suspect in this case is white and completely unknown to him."
The parents of the boy, who asked to remain anonymous, said he has been "the victim of crime and the victim of the system".
His father, who is appealing the decision, added: "I'm shocked that the system was so insensitive, to heap more anguish and suffering on a child who's trying to recover, understand his injuries and move on.”
The boy's head teacher, met Nick Gibb, the education minister, this week to discuss the case, while his Labour MP, Bambos Charalambous, said that he planned to write to the JCQ to complain.
The JCQ said that the policy was in order to be "fair to all students".
It added: "The boards have offered to provide honorary awards that can be used with colleges, employers and universities to explain the circumstances."