Pakistan is a frontline state against the global war on terrorism. In December 2014, an attack on a school in Peshawar, Pakistan killed more than 130 students. In response, the Government of Pakistan established military courts to conduct trials of those suspected of terrorism-related offences. This measure may be viewed as a necessary evil – a temporary measure to speed up the trial process. On the other hand, it breaches human rights guarantees such as the right to a fair trial and undermines the separation of judicial power. Therefore, it cannot be a desirable long-term solution to terrorism. From a global perspective, the issue confronting Pakistan is one shared by other States confronting the scourge of terrorism: should national security and public safety trump other human rights? Even so, should the Pakistani government continue on its path of prioritising national security at the expense of civil liberties and various constitutional rights? And, if so, are there controls and a system of checks and balances over the powers of the government security organisations? Ultimately, I argue that the establishment of military courts is justifi ed, albeit an ‘antibiotic’ solution to larger systemic deficiencies in the justice system.