A 2‐year‐old, male, entire Eudyptula minor, kept in a colony of little penguins, started displaying neurological signs, including stumbling, shaking and ear scratching. Several treatment trials proved unsuccessful, and previous computed tomography failed to yield images of diagnostic quality. Due to the ongoing progression of the disease, the penguin was presented for general anaesthesia for magnetic resonance imaging. On presentation, a full neurological examination was conducted, the abnormalities were localised to vestibular apparatus or cerebellum, with a top differential diagnosis of bilateral otitis interna. The patient was scheduled for general anaesthesia to facilitate magnetic resonance imaging of the brain. There are limited reported data on anaesthesia of little penguins. When anaesthetising this species, there are multiple pre‐anaesthetic considerations: fasting period, availability of suitable monitoring, the presence of a tracheal septum, positioning of the patient, challenging intravenous access and complications such as alterations in normal body temperature and environmental temperature.