Captive breeding is fundamental to recovery programs for many endangered species. Most programs seek to maximise retention of genetic variation and minimise inbreeding risk by assigning individuals to pre-determined pairings, but the reproductive outcomes of such pairings are often poor. There is evidence that pairing individuals in captivity that are instead genetically and behaviourally compatible can result in improved reproductive success, and that the resulting offspring perform better when released into the wild. Evidence is also mounting that such compatible outcomes can be achieved by allowing female mate choice. We investigated whether the reproductive success of captive endangered eastern barred bandicoots (Perameles gunnii) improved when females were permitted to choose their mate. Over a 21day period, we allowed females to simultaneously evaluate two males that were unrelated to the female via interaction through perforated clear acrylic barriers, which permitted visual, auditory and olfactory, but not physical, contact. We determined female preferences by measuring how much time they spent interacting with each male, and whether they showed behavioural signs of receptivity. We then paired females with either their preferred or non-preferred male, and recorded the time to conception and number of pouch young produced. Based on the interaction choice trials, females paired with preferred males were significantly more likely to produce young (p=0.03). These preferred pairings also resulted in earlier conception of young than non-preferred pairings (p=0.008). These findings could improve productivity of the eastern barred bandicoot breeding program and, more generally, support the incorporation of mate choice into conservation breeding programs for other species wherever practical.