ObjectivesTo analyse how previous comorbidities, ethnicity, regionality and socioeconomic development are associated with COVID-19 mortality in hospitalised children and adolescents.DesignCross-sectional observational study using publicly available data from the Brazilian Ministry of Health.SettingNationwide.Participants5857 patients younger than 20 years old, all of them hospitalised with laboratory-confirmed COVID-19, from 1 January 2020 to 7 December 2020.Main outcome measureWe used multilevel mixed-effects generalised linear models to study in-hospital mortality, stratifying the analysis by age, region of the country, presence of non-communicable diseases, ethnicity and socioeconomic development.ResultsIndividually, most of the included comorbidities were risk factors for mortality. Notably, asthma was a protective factor (OR 0.4, 95% CI 0.24 to 0.67). Having more than one comorbidity increased almost tenfold the odds of death (OR 9.67, 95% CI 6.89 to 13.57). Compared with white children, Indigenous, Pardo (mixed) and East Asian had significantly higher odds of mortality (OR 5.83, 95% CI 2.43 to 14.02; OR 1.93, 95% CI 1.48 to 2.51; OR 2.98, 95% CI 1.02 to 8.71, respectively). We also found a regional influence (higher mortality in the North—OR 3.4, 95% CI 2.48 to 4.65) and a socioeconomic association (lower mortality among children from more socioeconomically developed municipalities—OR 0.26, 95% CI 0.17 to 0.38)ConclusionsBesides the association with comorbidities, we found ethnic, regional and socioeconomic factors shaping the mortality of children hospitalised with COVID-19 in Brazil. Our findings identify risk groups among children that should be prioritised for public health measures, such as vaccination.