In 2012, a wild boar (Sus scrofa) tuberculosis (TB) control programme was set up in a wild boar farm by means of intramuscular (IM) vaccination with a heat‐inactivated Mycobacterium bovis vaccine (IV). The goal was to assess safety and efficacy of the parenterally administered IV in a large farm setting with natural M. bovis circulation. Based on preceding results under laboratory conditions, we hypothesized that vaccinated piglets would show smaller scores of TB‐compatible lesions (TBCL) than unvaccinated controls. After vaccination, no adverse reactions were detected by visual inspection or at post‐mortem examination (n = 668 and 97, respectively). Post‐mortem data on TBCL were available for 97 vaccinated wild boar and 182 controls. The observed TBCL prevalence was 4.1% (95% CI = 0.2–8%) and 12.1% (95% CI = 7.1–17.1%) for vaccinated and control wild boar, respectively (P < 0.05). Among those animals with TBCL, no difference in the mean lesion score was found (P > 0.05). The results show that IV administered intramuscularly to wild boar piglets is safe and protects vaccinated individuals (66% reduction in TBCL prevalence) against natural challenge in a low‐prevalence setting. In a context of increasing TB prevalence in wild boar in Mediterranean habitats, vaccination achieved a progressive though slow decline in lesion prevalence since the onset of the vaccination scheme. Hence, vaccination might contribute, along with other tools, to TB control in wild boar and in pigs.