In the present study, we aimed to explore gender differences in infant mortality and neonatal morbidity in mixed-gender twin pairs. Data were obtained from the US National Center for Health Statistics Linked Birth-Infant Death Cohort. A total of 108,038 pairs of mixed-gender twins were included in this analysis. Among the mixed-gender twins, no significant difference in the odds of fetal mortality between male twins (1.05%) and female co-twins (1.04%). However, male twins were at increased odds of neonatal mortality (adjusted OR 1.59; 95% CI 1.37, 1.85) and overall infant mortality (adjusted OR 1.43; 95% CI 1.27, 1.61) relative to their female co-twins. Congenital abnormalities (adjusted OR 1.38; 95% CI 1.27, 1.50) were identified significantly more frequently in male than female twins. Moreover, increased odds of having low 5-minute Apgar score (<7) (adjusted OR 1.15; 95% CI 1.05, 1.26), assistant ventilation >30 minutes (adjusted OR 1.31; 95% CI 1.17, 1.47), and respiratory distress syndrome (adjusted OR 1.45; 95% CI 1.26, 1.66) were identified in male twins relative to their female counterparts. The results of our study indicated that in mixed-gender twin pairs, the odds of infant mortality and neonatal morbidity were higher in male twins than their female co-twins.