AimWhile associations between vitamin D deficiency and neurodevelopmental disorders have been found, large studies on child vitamin D, neurodevelopment, and sex differences among the general population are lacking. This study aimed to investigate the association between child serum 25‐hydroxyvitamin D (25(OH)D)) levels and neurodevelopmental problems (NDPs).MethodsSerum 25(OH)D and NDPs were measured at age two among the subcohort study of the Japan Environment and Children's Study. NDPs were assessed with the Kyoto Scale of Psychological Development 2001 (Kyoto scale). Adjusted odds ratios (aORs) for the Kyoto‐scale developmental quotient scores <70 were calculated, for postural–motor, cognitive–adaptive, and language–social domains and overall scores, adjusted for test month, latitude, small for gestational age, maternal age, and daycare attendance.ResultsAmong 2363 boys and 2290 girls, boys had higher 25(OH)D levels, but scored lower in the Kyoto scale. For boys in the vitamin D deficiency (<20 ng/mL) group, aORs of scoring the Kyoto‐scale DQs <70 were 2.33 (p = 0.006) for overall DQs, 1.91 (p = 0.037) for cognitive–adaptive, and 1.69 (p = 0.024) for language–social domains. For girls, results were inconclusive.ConclusionOnly boys showed a clear and cross‐modal association between vitamin D deficiency and NDPs.