Koala (Phascolarctos cinereus) joey rescues are increasing over the years, and rehabilitation of a joey requires extensive care, close proximity and handling by humans. These novel environments are likely to present a suite of biotic and abiotic stressors during rehabilitation. In this study, we longitudinally monitored the faecal cortisol metabolites (FCMs) of three koala joeys within the context of potential stressors at the Magnetic Island Koala Hospital, Queensland, Australia. A total of 92 faecal samples were analysed for FCMs using a polyclonal R4866 cortisol enzyme-immunoassay which has been previously validated in koalas. The iterative baseline method was used to establish FCM profiles of all individuals, and to identify significant peaks in FCM concentrations. Visitor events were identified and confirmed as an acute stressor based on the FCM profiles of the koala joeys. All three koala joeys elicited a significant rise in FCM concentrations after each visitor encounter. To our knowledge, this is the first study to report on the acute stress response of koala joeys to visitors. We recommend that visitor encounters be kept to a minimum, and perhaps avoided altogether especially for joeys that are being rehabilitated to be released back into the wild.