Prior research studies suggest that maternal polyunsaturated fatty acids could have protective effects on neurodevelopmental outcomes. The objective of this study was to examine associations between maternal polyunsaturated fatty acid intake during pregnancy and risk for autism spectrum disorder and other non-typical development in a prospective cohort. Eligible women already had a child with autism spectrum disorder and were planning a pregnancy or were pregnant with another child. Children were clinically assessed longitudinally and diagnosed at 36 months. Maternal polyunsaturated fatty acid intake during pregnancy was estimated using food frequency questionnaires. Maternal third-trimester plasma polyunsaturated fatty acid concentration was measured by gas chromatography. In all, 258 mother-child pairs were included. Mothers consuming more total omega-3 in the second half of pregnancy were 40% less likely to have children with autism spectrum disorder (relative risk = 0.6, 95% confidence interval: 0.3-0.98). No significant associations were observed between maternal third-trimester plasma polyunsaturated fatty acid subtype concentrations and risk of autism spectrum disorder. However, higher plasma eicosapentaenoic acid and docosahexaenoic acid concentrations were associated with lower non-typical development risk (relative risk ranging from 0.47 to 0.88). This study provides suggestive evidence of associations between risk of autism spectrum disorder in the children and maternal omega-3 intake in late pregnancy but not with third-trimester plasma polyunsaturated fatty acids. Further research is needed to evaluate these potential relationships.