Due to globalization, sub-Saharan Africa (SSA) is experiencing some changes in her traditional family patterns. A large body of research has examined the relationship between family structure and youth developmental outcomes and few studies have reported the gender differentials in the effect of changing family structure on these outcomes. In an increasingly knowledge-based globalized world, educational achievement is critical for the development of youth. This exploratory study examines the gender differences in the effect of family structure on educational outcomes of youth in Nigeria. We used the 2010 Nigeria General Household Survey which is available through Integrated Public Use Microdata Series (IPUMS)--International, consisting of 14,178 males and 13,858 females. Family structure was a significant predictor of youth educational outcomes, and there were significant gender differentials. There was a negative relationship between living with neither parent and ever enrolling among males and females, but the effect was much stronger for females. Interventions should focus on improving existing resources and place youth who are living with neither parents and are unmarried in stable and friendly environments through mentorship programs and community caregiver support. Programs should also engage community leaders continuously about the consequences of early marriages among female youth.