Acute high dose administration of the artemisinin antimalarial, beta-arteether (AE), was evaluated in rats using an auditory discrimination task (ADT) and histology. After rats were trained on the ADT, AE (25, 75, 125 mg/kg, im) or vehicle (sesame oil) was administered and behavioral performance was evaluated for 11 consecutive days. Histological evaluation of the brains was performed using thionine and cupric-silver staining. Damaged cells were counted in specific brainstem nuclei of all rats and a qualitative analysis of the rostral-caudal extent of selected brains was performed. Behavioral performance was not significantly affected by any treatment although some evidence of disruption was observed, particularly after the largest dose. At 125 mg/kg, AE produced statistically significant neuropathology, including chromatolysis, in the nucleus trapezoideus and nucleus superior olive. AE at 75 mg/kg, produced significant neuropathology in the nucleus trapezoideus. Neither AE at 25 mg/kg, nor vehicle produced damage. Qualitative analysis revealed a pattern of neuropathology focused in the brainstem. The results show that, in rats, a single dose of AE can produce a pattern of brainstem neuropathology and that specific brainstem nuclei, including auditory nuclei, are particularly vulnerable. These results are consistent with, and extend, previous studies demonstrating brainstem neurotoxicity from repeated AE administration. Moreover, early detection of AE-induced neuropathology is problematic and may require selective examination of brainstem functions.