BCG remains the only possible prophylactic intervention against Buruli ulcer (BU). Estimating its public health impact on BU control is an important issue. We conducted a case-control study to investigate the vaccine effectiveness of routine BCG vaccine against BU in southern Benin. From August 2002 to August 2003, BCG vaccination status was obtained for 279 clinically diagnosed BU cases and 988 age- and sex-matched neighborhood controls. BCG coverage, which was estimated by the presence of a scar or a vaccination record, was 64.5% in cases and 67.2% in controls. There was no evidence of a protective effect of routine BCG vaccination against BU in southern Benin (vaccine effectiveness adjusted for socioeconomic status = 12%, 95% confidence interval = -24% to 37%).