The focus of this article is the court, constitution making relations in Pakistan and particularly the role played by the military courts in respect to human rights. Pakistan's military has played a dominant role in shaping the legal and political structure and Pakistan courts martial and had judicial reform and debate over the balance between national security and human rights exercised. The introduction of these concerns over due process and the military courts’ judicial independence since 2015 in Pakistan’s counterterrorism strategy has drawn alarm. Yet they were supposed to fight against the increasing terrorist and militant activities, also in contradiction with constitutional guarantees and were at loggerheads with transparency and accountability. It looks at what happens as Pakistan’s counterterrorism measures go against the basic foundations of justice and some recommendations that were made, to ensure that Pakistan’s counterterrorism steps comply with international human rights normative standards and have constitutional guarantees.