ABSTRACT Migrants often encounter heightened health risks during crises. We analysed the disparities in the burden of HIV between Japanese nationals and international migrants in Japan by comparing new HIV infections, AIDS cases, and HIV-related deaths between 2018–2019 (pre-COVID-19) and 2020–2021 (during the COVID-19 pandemic). Between 2018 and 2021, 4,705 new HIV infections were reported in Japan (2,813 Japanese nationals and 522 international migrants). Additionally, 1,370 AIDS cases (1,188 Japanese nationals, 182 international migrants) were recorded, representing 29.1% of the total. Comparative analysis of HIV incidence and mortality rates between Japanese nationals and international migrants indicates elevated disparities: During the COVID-19 pandemic, the HIV incidence rate among Japanese nationals decreased from 1.8 to 1.5 cases/100,000 people, while the rate among international migrants remained high at 12.8 cases/100,000 people. The AIDS incidence also increased for international migrants from 2.8 to 3.8 per 100,000 people, while Japanese nationals maintained a low at 0.5 per 100,000 people. International migrants living with HIV experienced a significantly younger age at death due to HIV-related illness (coefficient = −11.7, p < .01). The COVID-19 pandemic may have exacerbated the disparities with more international migrants living with HIV being diagnosed late and with less precise reporting. Investment in more equitable HIV care is warranted.