Primary nasopharyngeal mycobacteriosis is a rare disease. We present a case in which skull base bone erosion appeared and was alleviated during the course of the treatment. Bone complications occur in osteoarticular mycobacteriosis, but their occurrence in primary nasopharyngeal mycobacteriosis has not been reported. A 77-year-old immunocompromised Asian woman presented with a right occipitotemporal headache. An ulcerative mass covered with a thick yellowish discharge was found in the roof and posterior walls of the right nasopharynx. Because histopathological examination indicated the presence of mycobacterial infection, we began using antituberculosis medication for the treatment because of the possibility of primary nasopharyngeal tuberculosis. However, this was followed by glossopharyngeal and vagus nerve paralysis. Computed tomography (CT) showed a diffuse enhancing mucosal irregularity in the nasopharynx with bony erosion of the external skull base. Deep tissue biopsy was repeated to differentiate it from malignant lesions, and drainage of pus from the right nasopharynx was confirmed. Subsequently, the headache, neurological findings, and the yellowish discharge disappeared, and the bony erosion of the external skull base was alleviated. Surgical intervention should also be considered for drug-resistant mycobacteriosis. We concluded that mycobacteriosis should also be considered apart from carcinoma even if CT shows a diffuse enhancing mucosal irregularity with bone destruction in the nasopharynx.