A 31-yr-old male, captive harbor seal (Phoca vitulina) was evaluated for a 48-hr period of anorexia followed by the onset of seizures. A prolonged seizure failed to respond to anticonvulsant therapy and the animal was euthanized. At necropsy, no significant gross lesions were identified. Reverse transcriptase–polymerase chain reaction testing of brain samples was positive for eastern equine encephalitis virus (EEEV) RNA, and serum was positive for anti-EEEV antibodies by plaque reduction neutralization. Histopathologic evaluation revealed severe and multifocal encephalitis with leptomeningitis, characterized by neutrophilic infiltrates in neuropil, neuronal necrosis, satellitosis, neuronophagia, and perivascular cuffs of lymphocytes, macrophages, and neutrophils. Additionally there was moderate, multifocal, adrenal cortical necrosis. Immunohistochemical staining for EEEV demonstrated viral antigen within necrotic neurons and glial cells. Virus was isolated from frozen brain tissue, sequenced for comparison to other strains, and determined to be a typical North American strain. EEEV should be included as a possible cause of neurologic disease in harbor seals with compatible signs located in geographic regions where vector transmission of EEEV is encountered.