Background: Manganese (Mn) is an essential micronutrient for humans, the diet being the main source of exposure. Some epidemiological studies describe a negative association between prenatal Mn and later neuropsychological development, but results are inconsistent. The aim of this study was to explore the association between prenatal Mn exposure and neuropsychological development assessed at 4 years of age. Methods: Study subjects were 304 mother-child pairs from the Gipuzkoa cohort of the INMA (Environment and Childhood) Project. Mn was measured in newborns’ hair. Children’s neuropsychological development was assessed at 4 years of age using the McCarthy Scales of Children’s Abilities. Multivariate linear regression models were built. Stratified analysis by sex was performed. Generalized additive models were used to assess the shape of the relation. Results: The median Mn concentration in newborns’ hair was 0.42 μg/g (95% CI = 0.38, 0.46). The association between Mn levels and the neuropsychological development was not statistically significant for the general cognitive scale (β [95% CI] = 0.36 [−5.23, 5.95]), motor scale (β [95% CI] = 1.9 [−3.74, 7.55]) or any of the other outcomes. No sex-specific pattern was found. The best shape describing the relationship was linear for all the scales. Conclusion: Our results suggest that prenatal Mn concentrations measured in newborns’ hair do not affect cognitive or motor development at 4 years of age in boys or in girls at the observed Mn levels.