We aimed to determine the association between maternal bonding difficulty in the postpartum period and children’s neurodevelopment, considering maternal psychological distress and child sex-specific differences. To evaluate the relationship, the dataset of the Japan Environment and Children’s Study was used, as well as the Mother-to-Infant Bonding Scale (MIBS), the six-item version of the Kessler Psychological Distress Scale (K6) for mothers, and the Ages and Stages Questionnaires Third Edition for children aged 2 to 4 years. Maternal MIBS and K6 were administered at 1 year postpartum. Data from 24,798 boys and 24,025 girls were analyzed. Multivariate logistic regression analyses, with the reference groups being those with maternal MIBS scores ≤4 and K6 scores ≤4, were performed. The Benjamini–Hochberg procedure was employed to account for multiple testing. In boys, maternal bonding difficulty (MIBS score ≥5) without psychological distress (K6 score ≤4) was associated with a screen-positive result for neurodevelopmental delay in all five domains (communication, gross motor, fine motor, problem-solving, and personal-social) at ages 2 to 4 years. In girls, maternal bonding difficulty without psychological distress was associated with a screen-positive result for neurodevelopmental delay in all five domains at 2 years of age. However, at age 4 years, maternal bonding difficulty without psychological distress was no longer associated with a screen-positive result for problem-solving delay in girls. The association of maternal bonding difficulty without psychological distress at 1 year postpartum with screen-positive result for problem-solving delay persisted in boys, but at age 4 years in girls, the association no longer existed.