Recurrent pain is an increasing public health problem among school-aged children, with potential negative impact on children's daily lives, such as schoolwork. The overall aim of this study was to investigate whether recurrent pain in school year 6 was associated with poorer academic achievement at the end of elementary school in school year 9. The study was a follow-up study based on data from "The Study of Health in School-Aged Children from Umeå". Participants were 1567 children aged 12 to 13 years who attended school year 6. A follow-up was performed in school year 9, when the children were 16 years old. The children answered a questionnaire about recurrent pain (headache, stomachache, and backache). Information about academic achievement was collected from school registers. The results showed that having weekly recurrent pain in school year 6 predicted lower final overall grade points in school year 9 than in children with no recurrent pain. This applied for recurrent headache, stomachache, backache, and multiple pains and for both girls and boys. Recurrent pain did not predict secondary school eligibility, however. Perceived problems with academic achievement and problems with concentration partly mediated the association between recurrent pain and lower final overall grade points. Sleep problems were not associated with academic achievement and were therefore not a mediator. Thus, the results suggest that recurrent pain may predict later impairment of academic achievement and that problems with concentration and children's perceived achievement in school, but not sleep problems, may partly explain this relationship.