Miller Fisher Syndrome: This is a variant of Guillain-Barré Syndrome and is closely related to Bickerstaff Encephalitis, often presenting with similar symptoms such as ataxia, areflexia, and ophthalmoplegia. The key distinction lies in the presence of encephalitis in Bickerstaff, which may not be as pronounced in Miller Fisher Syndrome.

Guillain-Barré Syndrome: While not typically presenting with the encephalitic features seen in Bickerstaff Encephalitis, some forms of Guillain-Barré Syndrome can have central nervous system involvement, making it a consideration in the differential diagnosis.
Multiple Sclerosis: Especially in cases where the diagnosis of Bickerstaff Encephalitis is not clear-cut, multiple sclerosis could be considered due to its potential for presenting with a wide range of neurological symptoms, including encephalitis-like episodes.
Acute Disseminated Encephalomyelitis (ADEM): ADEM is a monophasic illness characterized by widespread demyelination in the brain and spinal cord, which can present similarly to Bickerstaff Encephalitis with symptoms of encephalitis and neurological deficits.

Brainstem Infarction: Given the potential for Bickerstaff Encephalitis to present with brainstem symptoms, missing a brainstem infarction could be catastrophic. Prompt imaging is crucial to rule out vascular causes.
Infectious Encephalitis (e.g., Herpes Simplex Encephalitis): These conditions require immediate antiviral treatment and can present with similar symptoms of encephalitis, making them critical not to miss.
Wernicke's Encephalopathy: This condition, caused by thiamine deficiency, can present with ophthalmoplegia, ataxia, and altered mental status, similar to Bickerstaff Encephalitis, and requires urgent treatment to prevent long-term damage.

Hashimoto's Encephalopathy: A rare condition associated with Hashimoto's thyroiditis, presenting with encephalopathy and sometimes seizures or stroke-like symptoms, which could be considered in the differential diagnosis of Bickerstaff Encephalitis.
Neuromyelitis Optica Spectrum Disorder (NMOSD): Although more commonly associated with optic neuritis and myelitis, NMOSD can rarely present with brainstem symptoms and encephalitis, making it a rare but important consideration.
Prion Diseases: Such as Creutzfeldt-Jakob disease, which can present with rapidly progressive neurological deterioration and could be considered in cases where the diagnosis remains elusive.