Pakistan has been under security threats since her inception, however, the challenges it is facing today is unique in nature. Intolerance in society has given birth to social conflict, uprising of extremism, militancy and terrorism. The causes of psychological and emotional imbalance may be social injustice or psychological warfare. Institutions fighting to counter the threat are prime victims facing heavy casualty both in terms of men and material. At the initial level of this qualitative research, etiology of increasing intolerance, conflict and violence are examined with evidence from behavior of the inhabitants whereas in later part, the corollary is discussed with suggested way forward. Data is collected through interviewing target folks, literature review and evidence from society. An endeavor is made to discuss the facts which generally the citizens of Pakistan overlook or avoid. The research is primarily addressed to the students of Social Sciences and Administrative sciences, who could play a vital role to reduce conflict and intolerance in the society. It will also be a social service to the nation, while working as a reference for future study on the subject as an effort is made to identify the weak links of the society.