Pakistan since more than a decade has been facing the challenge of internal security derived from religiously grounded militancy. More than seventy thousand civilian and military personnel have lost their lives. Religion in Pakistan have always been central within its polity and social fabric. In this context, the influence of religion on the policy matrix gain strength with the changing domestic and external events. The formation of religious elite along with the strategic and political developments in 1980s paved the way for a particular set of religious dogma to proliferate their set of beliefs through rigor and force. A society with weak infrastructure, poorly governed areas, institutional imbalance between military and civilians are generically more prone to extremist and radical manifestations, as happened in case of Pakistan. In addition to, these socio political and economic weakness within the society entrenched with staunch rigid beliefs amalgamated to form an anti-state agenda where militants in the tribal belt in post 2001 years control certain parts of the region to implement their self-crafted code of Sharia. In addition to it, on the external front, US intervention in Afghanistan became a pivotal incident in stimulating certain pockets of society which were already entrenched with the phenomenon of rigid and peculiar philosophy based on the vision of exclusion. This piece of research intended to find out the roots and shoots of religious militancy in Pakistan and how it affected the internal security of Pakistan. The high number of human fatalities, suicide bombings, attacks on governmental and military installations, educational institutes, political leadership, markets, and public transport explicates the deep rooted implications of militancy in Pakistan. Mosque, Imam bargah, church was symbolically targeted by the militants. It was the most tragic decade in the history of Pakistan when the most defense less unit of society, school children were brutally massacred in 2014. The containment and eradication of militancy had been on the top security agenda as Pakistan’s security, stability and sustainability is entrenched with the eradication of the menace of militancy.