American Indian and Alaska Native (AI/AN) individuals are more likely to die with COVID-19 than other groups, but there is limited empirical evidence to explain the cause of this inequity. The objective of this study was to determine whether medical comorbidities, area socioeconomic deprivation, or access to treatment can explain the greater COVID-19 related mortality among AI/AN individuals. The design was a retrospective cohort study of harmonized electronic health record data of all inpatients with COVID-19 from 21 United States health systems from February 2020 through January 2022. The mortality of AI/AN inpatients was compared to all Non-Hispanic White (NHW) inpatients and to a matched subsample of NHW inpatients. AI/AN inpatients were more likely to die during their hospitalization (13.2% versus 7.1%; odds ratio [OR] = 1.98, 95% confidence interval [CI] = 1.48, 2.65) than their matched NHW counterparts. After adjusting for comorbidities, area social deprivation, and access to treatment, the association between ethnicity and mortality was substantially reduced (OR 1.59, 95% CI 1.15, 2.22). The significant residual relation between AI/AN versus NHW status and mortality indicate that there are other important unmeasured factors that contribute to this inequity. This will be an important direction for future research.