The objective of this thesis is to develop a game theoretical model for analysis of the conflict in the bilateral relations of Afghanistan and Pakistan. The development of the model is preceded by historical and qualitative analysis of Afghanistan, its internal politics and consequent trajectory of relationship between Afghanistan and Pakistan. The model has been developed keeping in view the existence of a National Unity Government in Afghanistan and the conflict between Afghanistan and Pakistan on the issues of the Durand line and Taliban. The game theoretical model hence developed is structured as a two-level game which has the domestic game in Afghanistan at the level one and an inter-state game at the level two. Both games have different structures with the level one being an extensive game tree whereas for the level two of the game hyper-gaming has been deployed to account for the different perception the players may have about the same conflict. Although this thesis avoids using the formal mathematical notation, knowledge of basic game theory is a prerequisite.