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The study examines various issues in Pakistan-Afghanistan Relations in the context that emerged after 9/11. It argues that security maintenance and various development pursuits (political and economic) of both Pakistan and Afghanistan considerably rely upon cordial and mutually cooperative relations between these two immediate neighbours. However, there exists trust deficit and the war against terrorism has itself become an issue of major concern between the two countries. Afghanistan urges Pakistan to do more to defeat and stop the alleged extremist infiltrations into Afghan territory while Pakistan repeatedly denies such charges and holds Afghan government itself responsible for its failure to check cross border incursions and rebuilding of Afghan nation-state. Foreign powers especially Indian involvement, into Afghan internal affairs has affected her relations with Pakistan a lot. According to some analysts the situation has worsened to such an extent that its long term national interests has damaged especially in the post 9/11 era. This study argues that Pakistan and Afghanistan have unquestionable significance for each other. Geo-strategic, political, economic and other reasons make it compulsion for both the countries to have cordial relations in their respective vested interests and larger interests of peace in regional and international context. They can defeat and remove many ills being faced by the two potential nations of South Asia. But such a prospect would be neutralized by foreign powers if leadership of both the countries unsuccessfully tackles all outstanding issues in their bilateral relationship.