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Rationale: Extra-pulmonary tuberculosis (TB) has long been a diagnostic challenge for clinicians, often requiring extensive workup and invasive procedures, with the risk of significant complications. Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is a minimally invasive and highly accurate diagnostic modality for the evaluation of mediastinal and abdominal lymphadenopathy and masses. Several reports on the utility of EUS-FNA as a favorable method for diagnosing extrapulmonary TB have been published. Patient concerns: A 54-year-old man complained of intermittent melena. Diagnoses: 18 fluorine-fluorodeoxyglucose positron emission tomography/computed tomography revealed suspected carcinoma metastasis. EUS-FNA did not reveal any evidence of malignancy. Interventions and outcomes: Laparoscopy was performed, and frozen section pathology during surgery showed granulomas with focal necrosis. Mycobacterium tuberculosis polymerase chain reaction was positive, but acid-fast bacilli staining was negative. Anti-TB treatment was initiated, and the patient was advised to visit the local TB dispensary regularly. Lessons: The presence of atypical inflammation of inadequate material or non-representative samples of extra-pulmonary TB was observed on EUS-FNA cytology. Mycobacterium tuberculosis polymerase chain reaction and acid fast bacilli should be performed to diagnose TB because of its higher sensitivity.