The pygmy hippopotamus (Choeropsis liberiensis) is endangered in the wild and very little is known about its reproductive biology. In zoological facilities, this species experiences a number of reproductive issues that complicate breeding management, including a high rate of stillbirths and failure of many pairs to reproduce. We conducted a comprehensive study to evaluate reproductive cycles and pregnancy in this species using enzyme immunoassays (EIAs) for fecal hormone metabolite analysis. Fresh fecal samples were collected twice weekly for a one to three year period from 36 female pygmy hippos housed at 24 zoological institutions. Samples were analyzed in three separate laboratories. Three progestogen metabolite EIAs (Pg-diol: 5β-pregnane-3α,20α-diol 3HS:BSA; PdG: pregnanediol-3-glucuronide R13904; mono-P4: Quidel clone 425) and three estrogen metabolite EIAs (E2a: estradiol-17β-OH 17-HS:BSA; E2b: estradiol 17β R0008; E2c: estradiol 17β R4972) accurately reflected reproductive events. Average estrous cycle length was 31.8 ± 7.4 days based on estrogen metabolite peaks and 30.9 ± 7.3 days based on nadir to nadir progestogen metabolite concentrations. Cyclical patterns in both estrogen and progestogen metabolites were detected throughout the year, indicating a lack of seasonality. Estrogen metabolite peaks were also observed during pregnancy and lactation, suggesting that follicular development occurs during both reproductive states. Pregnancy was most reliably demonstrated by elevation in progestogen metabolites (Pg-diol or PdG) in the second half of gestation. Average gestation length based on breeding to calving date was 203 ± 4 days for 15 pregnancies. This comprehensive overview of the reproductive biology of the female pygmy hippo provides valuable data for guiding long-term breeding management for this endangered species and serves as a baseline for future studies addressing the potential influence of social structure, diet, body condition, and other husbandry factors on estrous cycling and reproduction.