Background Just a few studies to date have focused on headaches, quality of life, and academic performance in children. Objective Determine the effect of headaches on the life of schoolchildren and the association between headaches and academic performance. Methods We conducted a cross‐sectional study. One hundred and ninety‐five students from an elementary school were randomly selected out of 355 students aged from 10 to 15 years old. Semi‐structured interview, the P ediatric Q uality of L ife I nventory V ersion 4.0, the C hildren's D epression I nventory, and the S tate‐ T rait A nxiety I nventory were used. The variables relating to academic performance were obtained by consulting the academic records. Results Prevalence of headaches: headache: 97.3% (179/184); migraine: 51% (94/184); tension‐type headache: 33% (61/184); primary stabbing headache: 7.6% (14/184); unclassified headaches: 5.4% (10/184). Migraine (relative risk: 3.11; 95% confidence interval: 1.54‐6.30) and more severe headaches (relative risk: 7.93; 95% confidence interval: 2.65‐23.7) were associated with lower quality of life ( P < .01; multivariate logistic regression). More severe headaches were associated with lower grades in school ( P < .01; multiple linear regression). Variables relating to headaches were not associated with “failing the school year” ( P > .05; chi‐square test and F isher's exact test). Conclusion Headaches were found to be associated with lower quality of life and poor academic performance.