The objective of this study was to describe the effect of the third-generation GnRH antagonist, acyline, on ovarian follicular population and serum anti-Müllerian hormone (AMH) concentrations in female dogs. Four late anestrous bitches were administered 330 μg/kg SC acyline every 10 days for 60 days and followed up for 45 days. Blood samples were drawn on days -1, 15, 30, 45, 60, 75, 90 and 105 for AMH determination. Then, the females were ovariectomized and the excised ovaries were gross and histologically evaluated. The total ovarian follicles were counted. None of the female dogs presented estrus during treatment. Only one bitch presented an ovulatory estrus 20 days after treatment. The total number of ovarian follicles in these bitches was 96,200.10 ± 26,125.12, with 84.13%, 11.36%, 7.8% and 0.01% corresponding to primordial, primary, secondary and antral structures, respectively. Pretreatment AMH concentrations were 0.62 ± 0.17 ng/mL. This hormone varied throughout the study period (p < 0.01), diminishing to nadir values during treatment to then rapidly recover after its effect (0.2 ± 0.05 vs. 0.67 ± 0.22 ng/mL; p < 0.01). Acyline rapidly and reversibly prevented the initiation of cycling without affecting follicle count but diminishing serum AMH concentrations.