The court decided against intervening in the private school's decision on exclusion - a ruling that could have significance for other parental challenges over exclusions.
The boy's father had claimed that the expulsion from the special school, where his son had been placed by the London Borough of Greenwich, had been unfair, unlawful and irrational.
The father claimed that the procedure for expelling his son had not allowed time for any defence against the accusations listed against him.
The boy, whose name is being withheld, had been expelled from Muntham House school near Horsham, West Sussex, after accusations that he had pointed his fingers in the shape of a gun and threatened to shoot a teacher.
The court heard that the pupil had said: "You're dead. You'll get a bullet through the head. I've got the means to do it."
But the boy's father says that this was only a joke and should not have been grounds for expulsion - a claim rejected by teaching staff who said the threat had been taken seriously.
Despite noting that there were shortcomings in the expulsions process, the High Court in London ruled that "it would be unrealistic to expect the school" to re-admit the boy.
"The decision to exclude was well within the range of responses open to a reasonable governing body in the circumstances of the case," concluded Mr Justice Richards.