A 35-year-old woman with systemic lupus erythematosus on immunosuppressive drugs and a history of pulmonary tuberculosis with complete treatment 8 years ago presented with prolonged fever for 4 months and rapidly progressive cognitive decline for 3 months. Neurological examination showed impaired cognition, bilateral cogwheel rigidity, and fine postural tremor in both hands. Laboratory testing were unremarkable. Her brain imaging on T2/FLAIR exhibited non-enhancing hyperintense lesions involving left striatum, internal capsule, optic tract, and lateral geniculate nucleus, and right putamen. CSF analysis revealed mild pleocytosis with normal glucose and protein level. CSF comprehensive microbiological studies and autoimmune panels were negative. Autoimmune striatal encephalitis was suspected, and immunotherapies were given. However, her clinical course worsened, developing parietal lobe signs. Repeated brain imaging showed increased diffusion involving left basal ganglia and external capsule, right lentiform nucleus, and subcortical white matter of both parietal lobes. Despite another aggressive immunotherapies, her condition progressed, warranting a stereotactic brain biopsy to achieve a definite diagnosis. Her brain tissue pathology result was non-specific. Real-time PCR for M. tuberculosis complex was negative but positive for Mycobacterium sp. Line probe assay identifiedM. celatum. Brain tissue culture was negative. Of these, the final diagnosis was M. celatum encephalitis. Therefore, we discontinued immunotherapies and started anti-NTM treatment including isoniazid, rifampicin, ethambutol, and levofloxacin. During follow-up visit at 1 month, she was seizure-free, her persistent fever had resolved, and there was no evidence of seizure, reflecting that her clinical progression had stopped.