Tuberculous otitis media (TBOM) is a rare form of extrapulmonary tuberculosis. The secondary involvement of the temporomandibular joint (TMJ) from TBOM has hardly been reported. This article presents the clinical features, diagnosis and therapy of a rare case of tuberculous otitis media with TMJ involvement. The diagnosis of TBOM with TMJ involvement was definitely established by a positive Mycobacterium tuberculosis nucleic acid amplification test on the surgical biopsy specimen. The patient reported relief of otalgia and otorrhea following the surgery combined with anti-tuberculosis drugs. We highlight the importance of nucleic acid amplification in the diagnosis of TBOM when traditional staining and culture methods return negative results. Although TMJ tuberculosis secondary to TBOM is extremely rare, a combination of anti-tuberculosis therapy and timely surgical intervention is necessary for refractory cases.