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Abstract Background Hepatobiliary tuberculosis is a rare manifestation of Mycobacterium tuberculosis infection, especially in younger patients. The non-specific symptoms and signs as well as the lack of definite imaging characteristics often impedes diagnosis. Definite diagnosis of tuberculosiscan be obtained through histopathological examination; conventional anti-tuberculosis drugs and surgery are the most commonly recommended treatments. Case presentation A previously healthy 15-year-old rural adolescent male presented with a 2-month history of weight loss and fatigue. We strongly suspected a Klatskin tumor; therefore, exploratory laparotomy was performed. However, the microscopical findings revealed a granuloma consisting of epithelioid cells, caseous necrosis, and lymphocytic infiltration, indicating caseating granulomatous inflammation and yielding a final diagnosis of hepatic hilar tuberculosis. Conclusion Hepatic hilar tuberculosis is an extremely rare case; few physicians may have actually treated a case. This report therefore aims to improve the overall understanding of lymphatic tuberculosis of the hepatic hilum.