(1) Background: Leptospirosis, mainly determined by strains belonging to serogroup Sejroe, has a direct impact on the reproductive efficiency of ruminants, such as sheep. In Brazil, Leptospira santarosai serovar Guaricura, known to be able to chronically colonize the uterine environment, is of special note. Although vaccination minimizes the effects of acute disease, whether or not it can protect from renal colonization remains controversial, and its effects on the genital tract are unknown. In this context, the present study aims to investigate the efficacy of vaccination in the prevention of experimental genital leptospirosis. (2) Methods: Eighteen sheep were divided into three groups: one vaccinated with a polyvalent commercial bacterin, one vaccinated with an autologous bacterin, and one unvaccinated. After 14 days, the sheep were experimentally challenged with 108 leptospires (L. santarosai, serogroup Sejroe, serovar Guaricura, strain FV52) intraperitoneally. Serology and colonization of the urinary and genital tracts were carried out monthly by PCR for 210 days in all animals. (3) Results: Vaccination significantly elicited antibody titers with a predominance of agglutinins against serogroup Sejroe. Both urinary and genital infections were confirmed by PCR. Positivity in urine PCR was absent after D120, while genital infection persisted until the end of the study. Serological results and the finding that vaccination did not avoid renal colonization align with previous studies. Despite vaccination, Leptospira established chronic and asymptomatic colonization of the genital tract until D210, an outstanding finding that remains to be fully understood in its mechanisms. (4) Conclusions: This is the first study conducted to analyze the effects of vaccination in the prevention of genital leptospirosis.