Abstract Background Genome-wide polygenic scores for educational attainment (PGS-EA) and socioeconomic factors, which are correlated with each other, have been consistently associated with academic achievement and general cognitive ability in children and adolescents. Yet, the independent associations of PGS-EA and socioeconomic factors with specific underlying factors at the neural and neurocognitive levels are not well understood. The goal of this study was to examine the unique contributions of PGS-EA and parental education to cortical thickness (CT), cortical surface area (SA), and neurocognitive skills in children and adolescents. Methods Participants were typically developing children and adolescents (3-21 years of age; 53% male; N = 391). High-resolution, T1-weighted magnetic resonance imaging data were acquired. PGS-EA were computed based on the most recent genome-wide association study of educational attainment. Sustained attention, inhibitory control, working memory, vocabulary, and episodic memory were measured. Results PGS-EA and parental education were independently and significantly associated with SA, vocabulary, and attention outcomes but were not associated with CT. Vertex-wise analyses indicated that higher PGS-EA was significantly associated with greater SA in the left medial orbitofrontal gyrus and inferior frontal gyrus after accounting for parental education. Higher parental education was significantly associated with greater SA in the left parahippocampal gyrus after accounting for PGS-EA. Conclusions These findings suggest that education-linked genetics may influence SA, particularly in certain frontal regions, leading to variability in academic achievement. Results suggested genetic confounding in associations between parental education and SA in children and adolescents, with these associations remaining significant after controlling for PGS-EA.