Meningoencephalitis caused by aberrant trematode migration is described in two California sea lions (Zalophus californianus) admitted to a rehabilitation hospital between May and August 2001. Both animals displayed seizure activity and were euthanized due to poor response to therapy. Gross abnormal findings included liver flukes (Zalophotrema hepaticum) in the bile ducts and areas of swelling and necrosis in the cerebrum, cerebellum, and brain stem. Histopathology revealed meningoencephalitis with necrosis, hemorrhage, and many trematode eggs within the brain. In one sea lion, an adult trematode was found on the surface of the cerebrum. These are believed to be the first reported cases of meningoencephalitis caused by aberrant trematode migration in pinnipeds.