The sectarian violence got the moment during Zia's reign when the Deobandi sect created violent militant groups as Sipah-e- Sahaba and Lashkar-e-Jhangvi. In contrast, the Shia sect created Sipah-i-Mohammad Pakistan under the banner of the Afghan Jihad. Both Deobandi and Shia sects had ignited the violent clashes, which led to many innocent people's massacre. This moment of violent clashes was continued during the reigns of Benazir Bhutto and Nawaz Sharif, wherein the governments had ignored the violent activities of both religious factions. However, the incident of 9/11 had changed the dynamics of this violent conflict when the Musharraf government banned all militant groups for overcoming the extremism. This paper explores the polarization among the Deobandi and the Shias and their influence on Pakistan's national security. This paper suggests that the government should scrutinize all madrassas' curricula by removing hatred materials from the scheme of madrassas' study.