Background: Functional somatic symptoms (FSS), which commonly cannot be attributed to well-defined organic pathology, often co-occur with internalizing psychopathology and fluctuate throughout different life stages. We examined FSS courses throughout adolescence, and the association between preadolescent FSS, FSS severity and internalizing psychopathology at late adolescence. Methods: Data from the Copenhagen Child Cohort (CCC2000) were utilized from assessments at ages 11–12 years (preadolescence; T0) and 16–17 years (late adolescence; T1). Self-report questionnaire and interview data on FSS, internalizing psychopathology, chronic medical conditions, and sociodemographic data from Danish national registers were available for 1285 youths. FSS courses were categorized into persistent (high FSS at T0 & T1), remission (high FSS only at T0), incident (high FSS only at T1) or no FSS (no FSS at T0 & T1). Multiple linear and multinomial logistic regressions were conducted to investigate the FSS/psychopathology association. Results: 1.8% of adolescents fell into the persistent FSS course group throughout adolescence. Higher preadolescent FSS predicted FSS (b = 0.07, p <.001), anxiety (b = 0.05, p <.001) and depression (b = 0.06, p <.001) at age 16/17, even after controlling for sex, parental education, a chronic medical condition and internalizing psychopathology in preadolescence. Persistent, incident, and remittent FSS courses were associated with significantly higher mean levels of anxiety and depression compared to the reference group (no FSS). Conclusions: FSS during pre- and late adolescence might increase and co-occur with anxiety and depression throughout adolescence, potentially due to shared underlying risk factors and processes.