Youth (aged 10 to 24 years) comprise nearly one-third of Uganda’s population and often face challenges accessing sexual and reproductive health (SRH) services, with a disproportionately high incidence of negative SRH outcomes. Responding to COVID-19, Uganda implemented strict public health measures including broad public transportation, schooling, and business shut-downs, causing mass reverse-migration of youth from urban schools and workplaces back to rural home villages. Our study aimed to qualitatively describe the perceived unintended impacts of COVID-19 health measures on youth SRH in two rural districts.