Abstract Background Previous research has shown that vaccination reduces risk of post-COVID-19 venous thrombosis or embolism (VTE), but the effect of vaccine boosting on post-COVID-19 VTE risk reduction is unclear. We sought to estimate the effect of COVID-19 vaccination on the risk of post-COVID-19 VTE and to examine if the magnitude of this association differed among variant eras. Methods We performed a case-control study of Military Health Systems (MHS) beneficiaries who tested positive for SARS-CoV-2 in 2020-2022. Cases were defined as those with medically-attended VTE within 90 days after their first SARS-CoV-2 positive test; controls were defined as SARS-CoV-2 infections without incident VTE by 90 days. Multivariate logistic regression estimated the odds of post-SARS-CoV-2 VTE based on pre-COVID-19 vaccine status, adjusting for other VTE risk factors. Results A total of 4,646 MHS beneficiaries were included in this analysis; 1,370 received a primary vaccine series and a further 790 received at least one booster at time of infection; 71 had VTE within 90 days of SARS-CoV-2 infection. Those who were vaccinated had lower odds of VTE compared to the unvaccinated following infection (primary series: aOR 0.28, 95% CI 0.13-0.62, booster dose: aOR 0.06, 95% CI 0.01-0.46). Post-COVID-19 VTE risk was lowest during the Omicron era, but VTEs were too rare to examine for an interaction of variant era and vaccine effect. Conclusions Among MHS beneficiaries, COVID-19 vaccination was associated with a reduced risk of post-COVID-19 VTE diagnosis; estimated risk reduction was larger among those who received a booster.