The aim of this study was to assess the association between overweight and school performance among primary school children prospectively and including a broad range of potential confounding factors. In addition it was investigated what factors mediate this association. For this purpose, data of 2,159 12-year-old children who participated in the Prevention and Incidence of Asthma and Mite Allergy (PIAMA) birth cohort study were used. Two indicators of school performance were parental reported when children were 12 years of age and included (i): the score on a standardized achievement test that Dutch children have to complete at the end of their primary education (Cito)-test and (ii): the teacher's advice regarding a child's potential performance level in secondary education. Children's height and weight were measured by a trained research assistant at the age of 8 and by their parents at the age of 12. Overweight was defined using age and gender specific cut-off points. Multivariate regression analyses were performed to assess the association between overweight and school performance. Besides, both confounder and mediation analyses were conducted. Results showed lower Cito-test scores and lower teacher's school-level advice among overweight children. These associations were no longer significant when adjusting for parental educational level, skipping breakfast, and screen time. This study found no independent association between overweight and school performance among primary school children. Results showed strong confounding by parental educational level.