Tuberculosis in the otomastoid compartment is extremely rare. The classical presentation of tuberculous otitis media includes chronic otorrhea, severe hearing loss irrespective of the disease, multiple perforations, and pale granulations in the middle ear cavity. However, most present with non-specific signs and symptoms making it a diagnostic dilemma. Here, we report a case that presented with a bony mastoid cyst which is the first case report to the best of our knowledge. A 12-year-old boy visited our center with a complaint of chronic ear discharge and hearing loss not improving with conventional antibiotic therapy. The computed tomography scan of the temporal bone revealed soft tissue opacification in the mastoid along with features suggestive of cholesteatomatous chronic otitis media. The patient underwent mastoidectomy under general anesthesia, which revealed a bony mastoid cyst filled with turbid fluid along with granulation tissues in the middle ear cleft without cholesteatoma. Final histopathology revealed tuberculous otitis media. Antitubercular chemotherapy was started and the patient's condition recovered. Primary tuberculous mastoiditis is a rare clinical entity that requires a high index of suspicion. It can also present as chronic otorrhea with mastoid cyst, and thus need to be considered as one of the differential diagnoses.