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Separatist tendencies emerged in India and Pakistan even before the end of colonial rule in both countries in 1947. The political leadership of these states while dominating the political systems in their respective countries equally demonstrated much determination to curb the separatism. However their response to the challenge of separatist movements, particularly in Indian Tamil Nadu and Pakistani East Bengal, was different to each other. The outcome of separatist movements in two regions were altogether dissimilar. Indian leadership succeeded in repealing the Tamil Movement while Pakistani leadership fell short to the Bengali Movement. This paper is an attempt to expose that India and Pakistan both remained leader centred political systems during most of the time when they were confronted with the challenge of separatism in Tamil Nadu and East Pakistan respectively. While revealing the features of Tamil and Bengali Movement it compares the responses of Indian and Pakistani leadership to the challenges in their relevant spheres. The measures adopted by the political leadership of these countries to appease these movements have been explored in comparison with each other. The dealing of language issue, central to the separatism in both cases, has been specially assessed for the comparative study of response to challenge of separatism.