Australia has the highest small-mammal extinction rate in the world, and there are ample of reasons that have led to the higher extinction rates such as introduction of feral species, wildfires, climate change and uneven population distribution. All these factors instil a dire need to protect the species in captive environment. Stress has a major role to play in maintaining an adequate welfare conditions for wildlife, hence quantification of the stress levels in captive animals help us understand the effectiveness of the methods used to house the animals. In this study, we assessed the stress levels of captive marsupials namely Rufous bettongs (Aepyprymnus rufescens) (n=9), Long-nosed potoroo (Potorous tridactylus) (n=4) and Greater bilby (Macrotis lagotis) (n=5) by measuring the faecal cortisol metabolites using the Enzyme-Immuno assay (EIA) (R4866). We carried out a laboratory validation of the EIA for the Rufous bettongs and long-nosed potoroo by demonstrating parallelism between the pooled faecal samples and the standard curve. We also used the iterative baseline approach to calculate the baseline levels and detect peak concentrations of FCM in all the studied species. No significant differences were found in the FCM and baseline levels in the potoroos. Results highlighted a significant difference (p < 0.05) in the individual FCM and baseline levels of the bettongs. Additionally, significant differences (p < 0.05) were found in the FCM and baseline levels between male and female bettongs. In case of bilbies, the FCM and baseline levels showed no significant differences, however the male and female baseline levels were significantly different (p < 0.05). Our study provides the baseline and peak FCM concentrations in Long-nosed potoroos and Rufous bettongs under captive management. Future studies can use the iterative baseline approach and validated EIA to detect any possible variations in the FCM concentration and baseline values in captive marsupials created due to factors like sex, grouping, and housing conditions.