Fish oil contains omega-3 fatty acids, which play a vital role in fetal growth and development. In utero exposure to omega-3 fatty acids is exclusively dependent on maternal nutrition. Previous studies have suggested that prenatal fish oil supplementation has positive impacts on child neurodevelopment later in life. This study examines the associations between fish oil supplementation both before pregnancy and throughout pregnancy and subsequent child development. Mother–child pairs from the Upstate KIDS Study, a birth cohort consisting of children born between 2008 and 2010, were included. Self-reported prenatal fish oil supplementation data were available for 5845 children (3807 singletons and 2038 twins). At multiple time points, from 4 months to 3 years of age, child development was reported by the parents on the Ages and Stages Questionnaire (ASQ). Five developmental domains were assessed: fine motor, gross motor, communication, personal–social functioning and problem solving. Generalized linear mixed models were used to estimate odds ratios (OR) while adjusting for covariates. Primary analyses showed that the risk of failing the ASQ problem-solving domain was significantly lower among children of women who took fish oil before pregnancy (OR 0.40, 95% confidence intervals (CI) 0.18–0.89) and during pregnancy (OR 0.43, 95% CI 0.22–0.83). Gender interaction was not statistically significant, although stratified results indicated stronger associations among girls. Similarly, associations were primarily among singletons. Prenatal fish oil supplementation may be beneficial in regards to neurodevelopment. Specifically, it is associated with a lower risk of failing the problem-solving domain up to 3 years of age.