A 6-year-old Boxer was examined because of progressive neurologic signs, with severe hindlimb ataxia and head tilt on presentation. There was no history of diarrhea or vomiting. MRI of the brain revealed multifocal ill-defined T1-enhancing lesions affecting the cerebrum, brainstem, and cervical meninges, without associated mass effect. Meningoencephalitis was considered the most likely diagnosis. Multiple algae were observed on the cytology of the CSF and were most consistent withProtothecaspp. Antiprotozoal treatment was denied by the owners, and 5 weeks after diagnosis, the dog was euthanized due to progression of the neurologic deficits, and a necropsy was performed. Histological changes in the brain were compatible with severe multifocal protothecal meningoencephalitis. The specificProtothecaspecies was not identified. The gastrointestinal tract was unremarkable on histology. According to this report,Protothecaspp. should be included in the differentials for neurological deficits even in the absence of gastrointestinal signs.