This paper investigates the impact of female education on son preferences in Nepal. It analyzes changing trends in son preferences in children among Nepalese women from 1996 to 2022 based on data from the Nepal Demographic and Health Surveys (NDHS). Using multivariate and multilevel regression, the study explores the roles of both individual and contextual education in reducing son preference. In addition to individual female education, a novel contribution of this research is the identification of a compositional effect of education on son preference. Furthermore, the study investigates the relationship between women’s son preferences and their partner’s education to check whether the latter also influences the gender preference of women in children. The positive association between the compositional effect of higher education and lower son preference suggests the need for policymakers to prioritize female education as one of the key investments to reduce son preference. The results highlight the importance of future research on how education’s individual and compositional effects influence the sex ratio at birth. This is crucial for making informed decisions about including individual and compositional education effects in population projection models to better project future sex ratio at birth and population structure.