Conditional Cash Transfer (CCT) programs are one of the popular policy interventions in many developing countries to reduce poverty through human capital formation. Bangladesh is one of few countries which have been operating educational CCT Programs for more than two decades. Although many official documents have claimed that these programs contribute to educational indicators of the targeted groups, only a few empirical analyses were found in favour of this claim. Moreover, the findings of those analyses are biased due to using backdated and unrepresentative data or to the failure to use appropriate methods. Therefore, using empirical techniques of Propensity Score Matching (PSM), logit and ordered regression on the most recent waves of Household Income and Expenditure Survey (HIES) data of Bangladesh, this study investigated the impact of the Primary Education Stipend (PSP) and the Female Secondary Stipend (FSP) as well as the factors determining schooling choices. Results suggest that targeting in the case of PSP is weak and the stipend amounts in both the programs are insufficient to be commensurate with the out-of-pocket and opportunity cost of attending school. On the other hand, at both the primary and secondary stages, factors such as level of parental education, having a phone connection, involvement in child labour were found to be significant for enrolment. In addition, at the secondary level, child marriage phenomenon found to be significant. Stipend program alone is not enough to fight against this social hindrance in educating girls, especially in the rural areas.