X-linked agammaglobulinemia (XLA), also known as Bruton's tyrosine kinase (BTK) deficiency, is a primary antibody deficiency, characterized by low number of B cells, agammaglobulinemia and increased susceptibility to a variety of infections. Herein, we report a case of XLA with confirmed BTK mutation that developed neurological deficits. While we could not detect any responsible microorganism in spite of comprehensive workup, brain magnetic resonance imaging revealed moderate brain atrophy. The diagnosis of progressive encephalitis was made for this patient. Patients with XLA have a higher chance of encephalitis compared with other primary antibody deficiencies. Given the violent nature of encephalitis, it is a concern among XLA patients.