In this register-based real-life cohort study, changes in symptom-specific hospital contacts among 12–18-year-olds following two doses of the BNT162b2 COVID-19 vaccine compared to unvaccinated peers were investigated. Using national register data, vaccinated and unvaccinated adolescents were sex and age-matched each week during the inclusion period from May to September 2021. Symptom-specific hospital contacts covering ICD-10 R diagnoses were assessed before first the vaccine dose and after the second vaccine dose. Taking previous rates of symptom-specific hospital contacts into account, differences between vaccinated and unvaccinated adolescents were found. For some hospital contacts, higher rates were seen among the vaccinated, and for others, higher rates were seen among the unvaccinated. Unspecific cognition symptoms may be important to monitor in vaccinated girls, and likewise for throat and chest pain in vaccinated boys within the first months post-vaccination. In perspective, symptom-specific hospital contacts after vaccination against COVID-19 must be assessed by taking the risk of infection and symptoms following COVID-19 infection into account.