Abstract Introduction 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. Methods Semi-structured focus group discussions (FGD) and key informant interviews (KII) with purposively selected youth, parents, community leaders, community health worker (CHW) coordinators and supervisors, health providers, facility and district health managers, and district health officers were conducted to explore lived experiences and impressions of the impacts of COVID-19 measures on youth SRH. Interviews were recorded, transcribed, and coded using deductive thematic analysis. Results Four COVID-19-related themes and three subthemes resulted from 15 FGDs and 2 KIIs (n=94). Public transportation shutdown and mandatory mask-wearing were barriers to youth SRH care-seeking. School/workplace closures and subsequent urban youth migration back to rural homes increased demand at ill-prepared, rural health facilities, further impeding care-seeking. Youth reported fear of discovery by parents, which deterred SRH service seeking. Lockdown led to family financial hardship, isolation, and overcrowding; youth mistreatment, gender-based violence, and forced marriage ensued with some youth reportedly entering partnerships as a means of escape. Idleness and increased social contact were perceived to lead to increased and earlier sexual activity. Reported SRH impacts included increased severity of infection and complications due to delayed care seeking, and surges in youth sexually transmitted infections, pregnancy, and abortion. Conclusion COVID-19 public health measures reportedly reduced youth care seeking while increasing risky behaviours and negative SRH outcomes. Investment in youth SRH programming is critical to reverse unintended pandemic effects and regain momentum toward youth SRH targets. Future pandemic management must consider social and health disparities, and mitigate unintended risks of public health measures to youth SRH.