We sought to evaluate the impact of the COVID-19 pandemic on trends in chlamydia, gonorrhea, and pelvic inflammatory disease (PID) encounter rates within the Military Health System. This cross-sectional study queried electronic health records of 18- to 44-year-old female active duty service members and dependents during the pre-pandemic period (January 2018-February 2020), pandemic period 1 (March 2020-March 2021), and pandemic period 2 (April 2021-April 2022). We calculated monthly chlamydia, gonorrhea, and PID encounter rates using ICD-10 codes. We used change point analysis for trends in encounter rates and Poisson regression for differences in rates by age, active duty status, military rank, TRICARE region, and pandemic period. There were 36,102, 7,581, and 16,790 unique individuals with chlamydia, gonorrhea, and PID encounters, respectively, over the pre-pandemic and pandemic time frames. Chlamydia and gonorrhea encounter rates were highest in ages 18 to 19, in active duty service members, and junior enlisted compared to senior enlisted and officer sponsor rank. Chlamydia and gonorrhea encounter rates varied by TRICARE region. Chlamydia encounter rates were lower in both pandemic periods 1 and 2 compared to the pre-pandemic period, whereas gonorrhea encounter rates were lower only in pandemic period 2 compared to the pre-pandemic period. Trend analysis showed monthly chlamydia encounter rates did not significantly change from January 2018 through August 2020, and then decreased 2.4% monthly through the remainder of the study period (P < .05). Gonorrhea encounter rates did not significantly change from the beginning of the study period through February 2021 and then declined 1.9% monthly through the remainder of the study period (P < .05). Pelvic inflammatory disease encounter rates were highest in ages 18 to 19 and 20 to 24, in the TRICARE North region compared to the South region, in active duty service members compared to non-active duty, and in junior enlisted compared to senior enlisted and officer sponsor rank. Pelvic inflammatory disease encounter rates were lower in pandemic periods 1 and 2 compared to the pre-pandemic period. Pelvic inflammatory disease encounter rates declined 8.0% monthly from January 2020 through April 2020 (P < .05), followed by a 11.0% monthly increase from May 2020 through July 2020 (P < .05) and a 0.9% monthly decrease for the remainder of the study period (P < .05). Chlamydia, gonorrhea, and PID encounter rates in the Military Health System all declined in the pandemic period. Pelvic inflammatory disease was most influenced by the pandemic onset as demonstrated by an immediate decline in encounter rates followed by an increase several months into the pandemic. Young age, active duty, and junior enlisted status were associated with higher chlamydia, and gonorrhea, and PID encounter rates over the pre-pandemic and pandemic time frames. Lower encounter rates during the pandemic may be related to decreased access to health care services, reduced screening for sexually transmitted infections, or changes in sexual behavior. The less profound decline in gonorrhea encounter rates likely reflects the more symptomatic nature of gonorrhea compared to chlamydia. TRICARE regional differences varied for chlamydia, gonorrhea, and PID encounters.