Canine necrotizing meningoencephalitis (NME) is characterized by autoantibodies against glial fibrillary acidic protein (GFAP) in cerebrospinal fluids (CSFs). To clarify the time-course changes in autoantibodies, serial examinations were conducted in three dogs with NME (two Pugs and a Pomeranian) that were treated by immunosuppressive therapy. The Pugs retained high autoantibody titers throughout the observation periods (146 and 813 days) and died with neurological signs. On the other hand, the Pomeranian switched from being positive for autoantibody to negative after day 580, and its NME seemed to be in clinical remission until death on day 1238. Therefore, the anti-GFAP autoantibodies can be detected over time in canine NME even during immunosuppressive therapies. However, the autoantibodies can also disappear within a certain period after onset.