Higher education increases the likelihood of a healthy and successful life. This study investigated the association between relative deprivation and aspiration for college education in adolescents in Japan. The data of the 2016 survey of the Longitudinal Survey of Newborns in the twenty-first Century, a nationwide birth cohort study following infants born in Japan in 2001, was analyzed (the participants were 15 years old; n = 17,662). Their relative deprivation at 12 years of age, that is, the Yitzhaki index using the same municipality as the reference group, was derived from another national survey. Three-level multilevel logistic regression with random intercepts (level 1: individual; level 2: municipality; level 3: prefecture) was modeled to investigate the association between the Yitzhaki index and having an aspiration for college education, adjusting for gender, parents' educational attainment, absolute household income, perceived social support, and the size of the city of residence. Sixty-six percent of adolescents had an aspiration for a college education. A higher Yitzhaki index was significantly positively associated with having aspirations for college education after adjusting for all covariates (odds ratio: 1.18 per interquartile range-change scale; 95% confidence interval: 1.09, 1.28). The positive influence of relative deprivation was more substantial in adolescents with higher household income. The findings suggest that relative deprivation could motivate adolescents' educational aspirations, but it was more prominent among those with high income. Policies that support adolescents under poverty by converting their aspiration into higher educational achievement are required to break the cycle of poverty.