Obtaining a suitable mate is an integral part of reproduction, with sexual selection processes such as female mate choice resulting in both direct and/or indirect benefits. Here, we investigated whether olfactory driven female mate choice influenced reproductive success in captive fat-tailed dunnarts (Sminthopsis crassicaudata). Although females spent 67% more time with a preferred male’s scent, reproductive success was not influenced by assigned mate choice. Of the 10 (of 12) litters that survived to weaning, average litter size was higher for non-preferred pairings (3 ± 0.83) compared with preferred pairings (1.6 ± 0.60), with weaning success equal for both pairings. Analyses suggested that offspring sex ratios were influenced by mate choice, with females paired with their preferred mate having more daughters (81%) in comparison to non-preferred pairings (44%) and by paternal body condition, whereby females paired with males in better body condition produced more sons. In this species, altering offspring sex ratios in favour of daughters may be achieved by pairing with preferred males, and towards sons by pairing with males in better body condition. With the increasing need for captive breeding programs, these techniques may provide opportunities to correct sex ratio biases and incorporate natural mating systems into conservation programs.