Background: Bee venom acupuncture (BVA) is an effective treatment method for various diseases. Bee venom, however, can cause adverse effects, even rarely including life-threatening anaphylaxis, so safety-related evidence is required. In this study, we systematically estimated the incidence rate of anaphylaxis in response to BVA. Methods: We searched eight databases (MEDLINE (Pubmed), EMBASE, Cochrane Central Register of Controlled, KISS, KMBASE, Koreamed, OASIS, and NDSL) and systematically reviewed the articles that met the inclusion/exclusion criteria. Results: Among 225 potentially relevant articles, 49 were selected for this study. The overall incidence rate of anaphylaxis in response to BVA was 0.045% (95% CI 0.028–0.062). Women (0.083%, 95% CI 0.010–0.157) showed a higher incidence rate than men (0.019%, 95% CI −0.018 to 0.055), while the incidence for patients who had a skin test conducted (0.041%, 95% CI 0.011–0.072) was not significantly different compared to that obtained for patients for which there was no information about a skin test (0.047%, 95% CI 0.026–0.067). The publication year affected the incidence rate: it was highest before 1999 (1.099%, 95% CI −1.043 to 3.241), lower between 2000 and 2009 (0.049%, 95% CI 0.025–0.073), and lowest between 2010 and 2021 (0.037% 95% CI 0.014–0.060). Conclusions: In this study, we provide reference data about risk size and factors of BVA-related anaphylaxis, which is essentially required for BVA application in clinics.