Autoimmune encephalitis (AE) is a severe inflammatory disease of the brain. Patients with AE demonstrate amnesia, seizures, and psychosis. Recent studies have identified numerous associated autoantibodies (e.g., against NMDA receptors (NMDARs), LGI1, etc.) involved in the pathogenesis of AE, and the levels of diagnosis and treatment are thus improved dramatically. However, there are drawbacks of clinical diagnosis and treatment based solely on antibody levels, and thus the application of additional biomarkers is urgently needed. Considering the important role of immune mechanisms in AE development, we summarize the relevant research progress in identifying cerebrospinal fluid (CSF) biomarkers with a focus on cytokines/chemokines, demyelination, and nerve damage.