Background: Head circumference (HC), the anthropometric index of both brain development and nutritional background, has been described to be significantly associated with scholastic achievement (SA). The aim of this study was to determine the impact of nutritional background and current nutritional status parameters on SA in the Education Quality Measurement System (SIMCE) tests. Methods: A representative sample of 33 schools was randomly chosen in the Metropolitan Region of Chile. The sample consisted of 1,353 school-aged children of both sexes, from the fifth grade of elementary school and from the first grade of high school who in 2009 took the SIMCE tests. Nutritional status was assessed through anthropometric parameters. Brain development was measured through the HC expressed as HC-for-age Z-score (Z-HC). Results: Students with Z-HC < -2 SD and >2 SD obtained low and high SA, respectively, both in the language and the mathematics tests (P < 0.001). In general, in both grades, those students with Z-HC ≥0 SD increase more than double the probability to obtain language and mathematics SA scores ≥ the median (P < 0.0001). Conclusion: We confirm the hypothesis that HC is the most relevant physical index associated with SA; therefore, children with the lowest scores in the SIMCE tests probably have lower brain development.