Intolerance has been a serious problem as an inter-communal problem and this problem exists in the form of inter-communal intolerance in Pakistan which leads to violence and bloodshed. Many factors contribute to this intolerance, including sectarian differences in belief and practice, political exploitation of sectarian differences, lack of education and understanding, and the influence of extremism. Due to which Pakistani people are facing many problems. There are many different sects of Muslims in Pakistan, each with its own set of beliefs and customs. These differences can sometimes lead to stresses and even violence between sects. For instance, the Sunni and Shia organizations of Islam have several views about the succession of the Holy Prophet (PBUH), and this has been a wellspring of contention between the two factions for a really long time. Misunderstandings and prejudices between sects can result from the fact that many Pakistanis lack Islamic knowledge. For instance, some individuals may be of the opinion that their particular sect is the only genuine Islamic sect and that all others are heretics. Intolerance and even violence can result from it. The aim of this research work is to explain a comparative analysis of intolerance among different Islamic sects in Pakistan and as well as to find out its causes and solution under the Islamic context. In this study used a qualitative approach to its investigation. The information was gathered from a variety of sources, including websites, books, magazines, news pieces, and research papers. The primary and secondary both sources were used in references. Any society that wants to sustain stability, moral development, and peace has to have a giving and tolerant relationship among its members of all religions and sects. To promote regional security, stability, peace, and order, it is equally important to behave with charity and tolerance. In Pakistan, where people of diverse countries, beliefs, and sects live, tolerance is especially important. There must be religious tolerance for people to coexist peacefully in society. Then the environment of society would be peaceful and calm.