Orphaned koala joeys constitute a substantial number of wildlife rescues. Mortality is highly prevalent in rehabilitating joeys, with little knowledge about the causes of mortality. The hypothalamic–pituitary–adrenal axis plays a vital role in mediating stress by producing glucocorticoids (e.g. cortisol), however, no studies have quantified glucocorticoids in koala joeys. Traditional cortisol enzyme immuno-assay (e.g. R4866) are limited in supply and are process intensive, whereas, modern enzyme immuno-assay (EIA) kits (e.g. Arbor Assay cortisol kit) are available world-wide and provide rapid results. Biological validation is unsuitable to be performed in recuperating joeys due to ethical considerations, hence, we compared the results from biologically validated R4866 assay with the commercially available Arbor Assay cortisol kit. Thirty-four faecal samples were collected, processed and analysed for faecal cortisol metabolites (FCM) using both, R4866 assay and Arbor Assay kit. The joeys presented a suite of clinical conditions which provided the natural variation in stress response for comparing the assay sensitivity and range. The results indicated that there were no significant differences between the FCM values measured by both the assays. Furthermore, the Bland-Altman plot indicated a very strong agreement between the FCM concentrations measured by the two assays. This study is only a step towards recommending the routine use of commercial kit in clinical settings with basic resources, for rapid quantification of stress in koala patients. It is crucial for future studies to perform laboratory validation procedures to confirm the efficacy of the commercial kit before practical use for FCM monitoring in koalas.