The Columbia Basin pygmy rabbit (Brachylagus idahoensis) is critically endangered and the focus of a captive-breeding program. However, reproductive success in captivity to date has not been sufficient to sustain reintroduction efforts. The goal of this study was to investigate patterns of fecal progestagen and glucocorticoid excretion in females during mating, gestation, and lactation and identify hormonal relationships to reproductive success. Fresh fecal samples were collected from 48 adult, female rabbits over 3 breeding seasons at a frequency of 4–7 samples per week. Results showed that a large (17-fold) increase in progestagen concentrations 1 day after mating provides a reliable means of determining if a successful mating occurred. In general, higher glucocorticoid concentrations during the breeding season, specifically during mating and gestation, were associated with lower reproductive success. Females that failed to conceive during the breeding season had higher glucocorticoid and lower progestagen baseline concentrations than females that did conceive. Glucocorticoid excretion during late gestation, but not lactation, was negatively associated with litter success, suggesting it affects offspring survival more during the prenatal than the postnatal period. Progestagen and glucocorticoid concentrations at the end of gestation were positively related to litter size, which may be an important factor in juvenile survival. In summary, higher concentrations of fecal glucocorticoids during the breeding season were associated with reduced conception rates and survival of subsequent litters. Ultimately, identifying what factors cause elevated glucocorticoids in pygmy rabbits could provide opportunities to alleviate negative stressors and increase the reproductive output of the captive population.