The Koala (Phascolarctos cinereus) is an endemic marsupial inhabiting four states of Australia. Urbanisation, declining habitat, drought and fires are threatening the survival of this flagship species. These threats may cause acute and chronic stress in koalas, which might also be associated with occurrence of infectious diseases in koala populations. Stress may induce an increase in cortisol reflected in increased faecal cortisol metabolite (FCM) values. To be able to use faecal cortisol metabolites to measure stress levels in this species, our aim was to determine baseline values for males and females during breeding and non-breeding season. A total of 351 defecations were collected fortnightly, twice a day, for 12 months from koalas at a wildlife facility in South East Queensland. Samples were analysed with three different enzyme immunoassays (EIAs): a cortisol, 5α-pregnane-3β,11β,21-triol-20-one (37e) and tetrahydrocorticosterone (50c) EIA. The latter, which also reacts with tetrahydrocortisol, the main metabolite in koala faeces, was found to have the highest biological sensitivity and, therefore, is the most suitable EIA to measure stress levels in koalas. Utilising this EIA, we found significant differences (p < 0.05) in FCM values between males and females, breeding and non-breeding season, and between morning and evening samples. Values of faecal cortisol metabolites established in stress-free koalas in this study can serve as a reference for future studies in koalas.