The purpose of this study was to investigate the impact of income inequality and parental socioeconomic status on several birth outcomes in Japan. Data were collected on birth outcomes and parental socioeconomic status by questionnaire from Japanese parents nationwide (n = 41,499) and then linked to Gini coefficients at the prefectural level in 2001. In multilevel analysis, z scores of birth weight for gestational age decreased by 0.018 (95% confidence interval (CI): -0.029, -0.006) per 1-standard-deviation (0.018-unit) increase in the Gini coefficient, while gestational age at delivery was not associated with the Gini coefficient. For dichotomous outcomes, mothers living in prefectures with middle and high Gini coefficients were 1.24 (95% CI: 1.05, 1.47) and 1.23 (95% CI: 1.02, 1.48) times more likely, respectively, to deliver a small-for-gestational-age infant than mothers living in more egalitarian prefectures (low Gini coefficients), although preterm births were not significantly associated with income distribution. Parental educational level, but not household income, was significantly associated with the z score of birth weight for gestational age and small-for-gestational-age status. Higher income inequality at the prefectural level and parental educational level, rather than household income, were associated with intrauterine growth but not with shorter gestational age at delivery.