Methods: Using the Military Health System Data Repository, we identified a retrospective open cohort of active duty servicemembers receiving care in the MHS from fiscal years 2018 to 2021. Through the use of ICD-10 diagnostic codes, all corresponding sexual assault care was identified for the cohort before (October 1, 2017 – Feb 28, 2020; pre-pandemic period) and after (Mar 1, 2020 – Sept 30, 2021; pandemic period) the institution of COVID-19 pandemic protective measures. Pre-pandemic and pandemic period rates of sexual assault associated encounters per 10,000 total health encounters were calculated by geographic location and compared using Wilcoxon’s sign rank test. Multivariate log binomial regression models were performed to estimate associated risk of sexual assault among active duty servicemembers and compared across both periods. Results: The study identified 47,067,073 encounters for servicemembers in the pre-pandemic period, of which 7,813 (0.016%) were associated with sexual assault. During the pandemic period, 4,377 (0.015%) of 28,926,480 encounters were associated with sexual assault, indicating a 44% reduction in total encounters and a 9% reduction in the proportion of encounters associated with sexual assault. 18 installations within the MHS had statistically significant increases in rates of encounters. Most sexual assault encounters occurred in the 20-24 year age, Female, White, Junior Enlisted, Army, and Unmarried categories. During both time-frames, younger age and being a female were associated with an increased risk of sexual assault encounters. Race, service branch, and marital status were also associated with the risk of encounters. Conclusion: Contrary to reports indicating a modest increase in the number of sexual assaults reported within the DoD, we found a reduction in the frequency of healthcare encounters associated with sexual assault during the pandemic which may be related to reduced access to care. Men comprised approximately 22% of sexual assault encounters while the racial distribution of sexual assault encounters approximates the estimates of the DoD published demographic statistics. This study illustrates that COVID-19 measures diminished access to care for sexual assault within the MHS but did not demonstrably alter the demographics of servicemembers seeking care. These findings suggest that the MHS may require contingency plans for future disruptions to care and changes in military posture.