The military courts were established after the deadly Peshawar school attack by the Taliban last year that killed 150 people mostly children.
These special courts have convicted several accused militants and at least four of them involved in the Peshawar attack were hanged last week.
A two-judge panel of the apex court headed by Justice Gulzar Ahmad suspended the execution of Haider Ali and Zahid Gul. The court also summoned the record of the trial of the accused by military courts.
The military courts only deal with cases of hardcore terrorists and they work in secrecy due to fear of backlash by the militants.
Cases of individuals are sent to the military courts for trial by the civilian government.
According to the military, the accused are allowed to have lawyers to defend them and they can also appeal against the punishment.
It is not for the first time that the supreme court has suspended a sentence by military courts.
