The COVID-19 pandemic has disproportionately affected persons in long-term care, who often experience health disparities. To delineate the COVID-19 disease burden among persons with intellectual disabilities, we prospectively collected data from 36 care facilities for 3 pandemic waves during March 2020–May 2021. We included outcomes for 2,586 clients with PCR-confirmed SARS-CoV-2 infection, among whom 161 had severe illness and 99 died. During the first 2 pandemic waves, infection among persons with intellectual disabilities reflected patterns observed in the general population, but case-fatality rates for persons with intellectual disabilities were 3.5 times higher and were elevated among those >40 years of age. Severe outcomes were associated with older age, having Down syndrome, and having >1 concurrent condition. Our study highlights the disproportionate COVID-19 disease burden among persons with intellectual disabilities and the need for disability-inclusive research and policymaking to inform disease surveillance and public health policies for this population.