Introduction Pediatric critical care patients with COVID-19 treated in Peru have higher mortality than those previously reported from other countries. Pediatric providers have reported a high number of patients without comorbidities presenting with hemorrhagic strokes associated with COVID-19. We present a study analyzing the factors associated with mortality in this setting. Methods Prospective case–control study that included patients <17 years old admitted to a pediatric critical care unit with a positive test confirming COVID-19. The primary outcome was mortality. Fisher’s exact test and the Mann–Whitney U test were used for the analysis. Results Forty-seven patients were admitted to critical care. The mortality of our study is 21.3%. The mortality of patients with neurological presentation was 45.5%, which was significantly higher than the mortality of acute COVID-19 (26.7%) and MIS-C (4.8%), p 0.18. Other risk factors for mortality in our cohort were strokes and comorbidities. Only one patient presenting with hemorrhagic stroke had an undiagnosed comorbidity. Conclusion Cerebrovascular events associated with COVID-19 in pediatric patients, including infants, must be recognized as one of the more severe presentations of this infection in pediatric patients. Impact Pediatric patients with COVID-19 can present with hemorrhagic and ischemic strokes on presentation. Neurological presentation in pediatric patients with COVID-19 has high mortality. Mortality of pediatric patients with COVID-19 is associated with comorbidities. Pediatric presentation and outcomes of COVID-19 in different regions can be novel to previously described.