New Zealand’s kākāpō parrot, once widespread, is now critically endangered due to habitat loss and introduced mammalian predators. Prior to major population decline, a unique kākāpō cestode, Stringopotaenia psittacea, was found in the 1880s and first described in 1904. Here we report the discovery of eggs of this cestode in kākāpō coprolites of pre-human settlement age from the Honeycomb Hill cave system, north-west Nelson. Analysis of 52 samples, including coprolites of post-human settlement age, from nine sites within six South Island locations across a wide geographic range, yielded only eight infected samples in this single cave system. Results suggest that prior to human settlement, S. psittacea was not widespread within and between kākāpō populations, in marked contrast to other parasite types of the extinct moa spp. Intense management of the last remaining kākāpō has endangered or possibly caused the extinction of this cestode. This is the first confirmed record of S. psittacea since its discovery in 1884.