This study investigates the impact of vaccination against SARS-CoV-2 on health outcomes and hospital contacts in children and adolescents aged 5–18 years infected with the SARS-CoV-2 Omicron variant, comparing previously vaccinated with unvaccinated. Using national register data, vaccinated and unvaccinated Danish children and adolescents with a positive SARS-CoV-2 test between 1 January and 31 March 2022 (Omicron dominance period) were included. The Prior Event Rate Ratio (PERR) was used to explore differences in hospital contacts (hospitalizations and emergency room (ER) visits), while Inverse Treatment Probability Weighted (IPW) risk ratios were used to explore the risk of severe health outcomes within six weeks following SARS-CoV-2 infection. Vaccinated 5–11-year-old girls had fewer visits to the ER compared to unvaccinated ones, PERR 0.92 (95% CI 0.84–1.00). Vaccinated 5–11-year-old boys had fewer hospitalizations (PERR 0.79 (0.64–0.99)) and more ER visits (PERR 1.13 (1.04–1.22)) compared to unvaccinated ones. An unadjusted and significant lower risk of febrile seizure among vaccinated 5–11-year-olds compared to unvaccinated ones was found (risk ratio 0.12 (0.04–0.39), p ≤ 0.01. No significant differences were found for severe conditions or for croup or pneumonia in either age group. The results indicate a modest protective effect of the vaccine in terms of hospital contacts, but no protective effect on health outcomes after SARS-CoV-2 Omicron infection in this population of Danish children and adolescents.