Background: Pediatric multiple sclerosis (MS) may hamper educational achievements due to psychiatric comorbidity and cognitive impairment. Our aims were to investigate school performance, psychiatric comorbidity, and healthcare utilization following pediatric MS and to differentiate between disability in MS and that arising from a non-brain-related chronic disease. Methods: We included all children (<18 years) with MS onset during 2008–2015 in Denmark with a medical record–validated MS diagnosis. The control groups were children from the general population or children with non-brain-related chronic diseases. Outcomes were register-based on 9–12 grade point average, psychiatric comorbidity, and healthcare visits. Results: Cohorts were children with MS ( n = 92), control children matched to children with MS ( n = 920), children with non-brain-related chronic diseases ( n = 9108), and “healthy” children with neither MS nor brain-related chronic disease ( n = 811,464). School performance in grades 9–12 was similar, but children with MS compared to those with non-brain-related chronic disease had an almost doubled hazard for psychiatric comorbidity (hazard ratio = 1.87; 95% confidence interval = 1.38–2.53; p < 0.0001) and a higher rate of all hospital visits ( p < 0.0001) but a lower rate of hospital admissions ( p = 0.001). Conclusion: Children with MS have a seemingly standard school performance but increased psychiatric comorbidity and a high rate of healthcare utilization.