GonaCon, a single-shot injectable immunocontraceptive vaccine targeting the gonadotropin-releasing hormone (GnRH), has been tested in key mammal species in the UK and shown to be a safe method to reduce population size in areas of high human wildlife conflict. Badgers exhibit an unusual reproductive physiology in that females may maintain fertilised eggs and dormant blastocysts at any time of year and delay their implantation until the winter. It is thus necessary to evaluate the consequences of delayed implantation and timing of vaccination on the effectiveness of GonaCon for fertility control of female badgers. We found that vaccination in June had an immediate effect on the fertility indicators monitored and inhibited subsequent cub production in the following year, while vaccination in November had no effect. Further results suggest that the optimal vaccination window in badgers could be as narrow as between June and August. The longer-term effectiveness of GonaCon vaccination in female badgers appears to reflect maintenance of anti-GnRH antibody titres at or above a putative threshold titre of 1:128,000, a threshold higher than that reported for other species (1:64,000). While it is possible that using a larger dose (> 1 mL) might lead to longer lasting effects, this study shows that vaccination would need to be repeated at least every 2 years in order to maintain levels of female infertility predicted to have demographic impacts on badger populations. Overall, no negative welfare consequences were observed in vaccinated badgers indicating that GonaCon is a potential tool for the management of conflicts involving badgers.