Previous research has shown that vaccination reduces risk of venous thrombosis or embolism (VTE) in hospitalized patients when pre-Delta and Delta SARS-CoV-2 variants were prominent. However, the effect of vaccine boosting on post-COVID-19 VTE risk reduction is unclear, particularly in Omicron variant infections, which have been associated milder severity than prior variants. We sought to estimate the effect of prior COVID-19 vaccination (including booster doses) on the risk of post-COVID-19 VTE and to examine if the magnitude of this association differed among the pre-Delta, Delta, and Omicron variant eras. To accomplish this, we performed a case-control study of military health system (MHS) beneficiaries who tested positive for SARS-CoV-2 in 2020-2022. Cases were defined as those with medically-attended VTE within 90 calendar 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. Stratified sub-analyses examined the risk and risk factors of post-COVID-19 VTE within each variant era (pre-Delta, Delta, and Omicron). A total of 5,266 MHS beneficiaries were included in this analysis; 1427 were fully vaccinated and a further 860 received at least one booster at time of infection; 71 (1.3%) had VTE within 90 days of SARS-CoV-2 infection. Those who were vaccinated and/or boosted had significantly lower odds of VTE compared to the unvaccinated following SARS-CoV-2 infection (fully vaccinated adjusted odds ratio [aOR] 0.27, 95% CI, 0.12-0.61; boosted aOR 0.07, 95% CI, 0.01-0.49). Post-COVID-19 VTE risk was lowest during the Omicron era (0.2%) compared to Delta (1.2%) or pre-Delta (2.0%) eras, but VTEs were too rare to examine for an interaction of variant era and vaccine effect on post-COVID-19 VTE risk. Among MHS beneficiaries, receipt of COVID-19 vaccination was associated with a reduced risk of COVID-19 VTE diagnosis; estimated risk reduction was larger among those who received a booster.