A 64-year-old woman with pemphigus was receiving treatment with steroids (prednisolone, 20 mg/day). The laboratory analysis revealed positive anti-Ach-R antibody, and thymoma with paraneoplastic pemphigus was diagnosed. Surgical resection of thymoma was canceled because preoperative chest computed tomography showed pulmonary nodules on the right S² and left S⁸ bronchial segments. End-bronchial washing was performed to culture the sample and rule out infection, but no pathogenic microbe was identified. Empiric antibiotic therapy was started. During the clinical follow-up, she complained of sensory impairment of the left upper limb, stagger, and diplopia. Brain magnetic resonance imaging revealed a brain stem abscess. During the same period, sputum culture was positive for Nocardia, and pulmonary nocardiosis was diagnosed. A change of antibiotics resulted in complete control and resolution of the lung and brain lesions.