Recurrent headache, abdominal and musculoskeletal pain are common in adolescents and it is therefore important to understand their impact on the transitional period from childhood to adulthood. However, studies of the prevalence over time and implications on educational outcomes are still limited, especially regarding multiple pain symptoms. The present study material consists of questionnaire surveys, completed in 2000 and 2008, including two study populations of 9th grade adolescents aged 15 living in West Sweden (n = 20 877). Pain symptoms and demographic variables were based on self-reports from the questionnaires, and school grades were obtained from Statistics Sweden after the student had finished their 9th grade. Between 2000 and 2008, the prevalence of abdominal pain increased among Swedish adolescents (largest increase in girls); the prevalence of headache increased only in girls; the prevalence of pain in upper body decreased only in boys. School grades were significantly lower among those with headache or abdominal pain. Among students with low school grades (10th percentile) the estimated difference between those having any of the symptoms or none were -27 school grade units (95% confidence interval for girls (-27.8; -26.0), for boys (-27.6; -25.5). Both symptoms being present pronounced the association. Low parental education increased the negative effect of symptoms on school grades, most pronounced in the group with the lowest grades. In conclusion, identification of pain symptoms may improve academic achievements, especially in students with multiple symptoms and with parents having low education. Further intervention studies are need.