Lockdown measures and the stress of the COVID-19 pandemic are factors associated with increased risk of violence, yet there is limited information on trends in emergency department (ED) encounters for sexual assault. To compare changes in ED encounters for sexual assault during the COVID-19 pandemic vs prepandemic estimates. This retrospective, population-based cohort study used linked health administrative data from 197 EDs across Ontario, Canada, representing more than 15 million residents. Participants included all patients who presented to an ED in Ontario from January 11, 2019, to September 10, 2021. Male and female individuals of all ages were included. Data analysis was performed from March to October 2022. Sexual assault, defined through 27 International Statistical Classification of Diseases and Related Health Problems, Tenth Revision, procedure and diagnoses codes. Ten bimonthly time periods were used to compare differences in the frequency and rates of ED encounters for sexual assault between 2020 to 2021 (during the pandemic) compared with baseline prepandemic rates in 2019. Rate differences (RDs) and age adjusted rate ratios (aRRs) and Wald 95% CIs were calculated using Poisson regression. From January 11, 2019, to September 10, 2021, there were 14 476 656 ED encounters, including 10 523 for sexual assault (9304 [88.4%] among female individuals). The median (IQR) age was 23 (17-33) years for female individuals and 15 (4-29) years for male individuals. Two months before the pandemic, ED encounters increased for sexual assault among female individuals (8.4 vs 6.9 cases per 100 000; RD, 1.51 [95% CI, 1.06 to 1.96]; aRR, 1.22 [95% CI, 1.09 to 1.38]) and male individuals (1.2 vs 1.0 cases per 100 000; RD, 0.19 [95% CI, 0.05 to 0.36]; aRR, 1.19 [95% CI, 0.87 to 1.64]). During the first 2 months of the pandemic, the rates decreased for female individuals (4.2 vs 8.3 cases per 100 000; RD, -4.07 [95% CI, -4.48 to -3.67]; aRR, 0.51 [95% CI, 0.44 to 0.58]) and male individuals (0.5 vs 1.2 cases per 100 000; RD, -0.72 [95% CI, -0.86 to -0.57]; aRR, 0.39 [95% CI, 0.26 to 0.58]). For the remainder of the study period, the rates of sexual assault oscillated, returning to prepandemic levels during the summer months and between COVID-19 waves. These findings suggest that lockdown protocols should evaluate the impact of limited care for sexual assault. Survivors should still present to EDs, especially when clinical care or legal interventions are needed.