A 58-year-old male farmer living in Binchuan County, Dali, Yunnan Province, was admitted to the First Affiliated Hospital of Dali University on July 20, 2022, with a complaint of “right upper abdominal pain for more than two days”. Routine blood tests showed elevated eosinophils counts (1.7 × 10⁹/L), erythrocyte sedimentation rate (ESR, > 120 mm/h), and blood chemical tests showed an increase in alanine aminotransferase (58 U/L), aspartate aminotransferase (74 U/L), gamma-glutamyltransferase (66 U/L) and alkaline phosphatase concentrations (257 U/L). Enzyme-linked immunosorbent assay (ELISA) measured strongly positive serum IgM and IgG antibodies against Fasciola hepatica, and the T-SPOT. TB test was tested positive. Abdominal plain plus enhanced computed tomography (CT) scans displayed the suspicion of hepatic malignancy with infectious diseases that failed to be excluded. Liver histopathology revealed tunnel-like necrosis and formation of foreign body granulomas, with F. hepatica infection and tuberculosis that cannot be excluded. Acid-fast staining of the left medial lobe liver specimen was positive, and Mycobacterium tuberculosis complex DNA was detected. Metagenomic next-generation sequencing (mNGS) of liver tissues detected 20 M. tuberculosis sequences and 15 F. hepatica sequences. The patient resided in Binchuan County, Dali Prefecture, Yunnan Province, where fascioliasis is prevalent, and had a habit of consuming raw or undercooked vegetables. Fascioliasis hepatica complicated by hepatic tuberculosis was diagnosed based on the patient’s epidemiological history, symptoms and signs, and auxiliary diagnosis results. Following deworming with triclabendazole at a dose of 15 mg/(kg·d) divided into 3 doses per day for 2 days and antitubercular therapy with rifampicin capsules (0.45 g once daily, adjusted for the patient’s weight of 48 kg), isoniazid tablets (0.3 g once daily), ethambutol tablets (0.75 g once daily) and pyrazinamide tablets (1.5 g once daily) for a week, the patient’s abdominal pain improved and was discharged from hospital. At the 3-month follow-up, liver enzymes returned to normal, and at the 6-month follow-up, the case had normal eosinophil counts, postoperative changes in liver segment 4 and strip-like dense shadows in surgical areas on plain abdominal CT scans, without remarkable progression.