The situation of Hindus and Sikhs as a persecuted minority is a little-studied topic in literature dealing with ethno-sectarian conflict in Afghanistan. Hindu and Sikh communities’ history and role in Afghanistan's development are examined through a structural, political, socioeconomic, and perceptual analysis of the minority populations since the country gained its independence in 1919. It traces a timeline of their evolving status after the breakdown of state structure and the ensuing civil conflicts and targeted persecution in the 1990s that led to their mass exodus out of the country. A combination of structural failure and rising Islamic fundamentalist ideology in the post-Soviet era led to a war of ethnic cleansing as fundamentalists suffered a crisis of legitimation and resorted to violence as a means to establish their authority. Hindus and Sikhs found themselves in an uphill battle to preserve their culture and religious traditions in a hostile political environment in the post-Taliban period. The international community and Kabul failed in their moral obligation to protect and defend the rights of minorities and oppressed communities.