Mortality is prevalent in koala joeys being hand reared/rehabilitated, with little knowledge about the causes of such high rates of mortality. Wildlife hospitals/rehabilitation expose koala joeys to novel husbandry environments that create stressful stimulus for these animals. Furthermore, loss of the mother and/or being raised by a human can be threatening and/or stressful. The hypothalamic–pituitary–adrenal axis plays a vital role in mediating the stress endocrine response of vertebrate species including marsupials (by adrenocortical release of glucocorticoids such as cortisol), however, there are no studies that quantify cortisol metabolites in koala joeys. To contribute to this dearth of knowledge, the primary aim of this study was to quantify the levels of faecal cortisol metabolites (as an index of physiological stress) in koala joeys undergoing rehabilitation. A total of 39 faecal samples were collected from four koala joeys admitted at a wildlife hospital in New South Wales, Australia. The samples were processed and analysed for faecal cortisol metabolites (FCM) using a polyclonal R4866 cortisol enzyme-immunoassay which has been previously biologically validated in adult koalas. The results indicated that there was significant inter-individual variation in FCM concentrations among the joeys, however, these differences were not based on the sex of the joeys. The average FCM concentration among joeys varied from 18.34 to 44.18 ng/g. Our study provides the first record of physiological stress in male and female rescued koala joeys by indexing FCM concentrations during rehabilitation.