The Supreme Court in its 182-page decision ruled the appellants had not proved that the military violated their constitutional rights or failed to follow procedure.
The decision is major blow to lawyers and civil society activists who had been struggling to reverse the convictions by the military courts.
A five-member full bench, headed by Chief Justice Anwar Zaheer Jamali, had reserved judgement on the appeals of the convicts on June 20.
They were tried by special military courts set up after Peshawar school attack for speedy trial of rebels.
It is not known when they were convicted and where the trial was held as such courts work at secret places due to security issues.
Army chief General Raheel Sharif had already rejected the appeals but the convicts had challenged the sentences in the Supreme Court.
The decision marks the first time the highest court has ruled on the legality of cases tried by the military.
She argued that they do not know under what law her client was taken into custody and whether due course of law was provided.
She again contended that people were illegally arrested under the regulation, and later the constitutional amendment was introduced to hide the illegality.
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