Central nervous system (CNS) tuberculosis mainly manifests as tuberculous meningitis and intracranial tuberculosis; intramedullary tuberculosis is uncommon. Scrub typhus is an acute naturally occurring infectious disease caused by Orientia tsutsugamushi. CNS tuberculoma following typhus is rare. The present study described a 60-year-old man with high fever, muscle soreness, yellowish skin and sclera and hepatosplenomegaly. At first, the patient was diagnosed with scrub typhus, after treatment with doxycycline he recovered completely. However, half a month after discharge, the patient experienced headache, night sweats and anorexia. Tuberculosis-specific enzyme-linked immunospot assay showed positive Mycobacterium tuberculosis antibody in cerebrospinal fluid (CSF). Metagenomic next-generation sequencing detected the presence of Mycobacterium tuberculosis in CSF. Magnetic resonance imaging of the brain and spinal cord showed multiple rings enhancing lesions in the cerebral hemispheres, cerebellum, brainstem and spinal cords. After the diagnosis of CNS tuberculoma, the patient was started on conventional anti-tuberculosis therapy resulting in a good prognosis.