Background: Adolescents lack adequate knowledge, self-efficacy, and access to sexual and reproductive health services; thereby, predisposing them to sexual violence, sexually transmitted infections, early marriage, and high fertility rates. Socio-economic inequalities fuel such problems, but we have limited evidence from some of the least developed states of Eastern India. Therefore, we aimed to assess the inequalities in the reproductive health knowledge and practices of unmarried adolescents (10-19 years) from marginalized populations in one district each from the state of Bihar and Assam in India.Methods: It was a community-based cross-sectional study with a quantitative research methodology. In our study, we captured data on five domains related to reproductive health, including knowledge about HIV/AIDS, and contraceptives, awareness and perceptions related to right age at marriage, general self-efficacy, menstrual hygiene practices among girls, and access to health services for reproductive health problems; besides socio-demographic details. We performed a 2-step cluster analysis to gain insights into the patterns of reproductive health knowledge and self-efficacy among unmarried adolescent boys and girls, separately. Multinomial logistic regression analysis was employed to identify the predictors associated with the cluster membership determined through cluster analysis.Results: A total of 811 boys and 826 girls participated in the study. Three-clusters were identified for boys and girls in the analysis, varying from high to low knowledge and self-efficacy for boys, and high to low knowledge with constant low self-efficacy in all the three clusters for girls. Higher educational status and increasing age were positively associated with the high knowledge clusters among boys and girls. Additionally, marginalized social class and working status were associated with higher knowledge cluster in girls.Conclusions: We emphasize on the need of comprehensive (covering a broad range of reproductive health issues, such as child marriage, contraceptives, HIV/AIDS, menstrual hygiene, etc.), contextualized (relevant for adolescents in the least developed states like Bihar), and customized (tailored for different cultures and religions through appropriate means) sexual and reproductive health education for adolescents.