Background <p>Alveolar echinococcosis (AE) is a rare but potentially fatal zoonotic disease that primarily affects the liver, while extrahepatic involvement usually indicates advanced disease and poor prognosis. Vertebral and pulmonary AE may closely mimic tuberculosis (TB), particularly in TB-endemic regions, leading to substantial diagnostic challenges. We report a case of late vertebral and pulmonary AE after previous hepatic hydatid surgery that was initially misdiagnosed as spinal and disseminated pulmonary TB.</p> Case presentation <p>A 28-year-old Tibetan woman from a nomadic family presented with a 7-month history of progressive back pain and a 2-month history of cough. She had undergone hepatic hydatid cyst resection 8 years earlier with antiparasitic therapy and had completed treatment for pulmonary TB 3 years previously. She also reported household exposure to active TB. Spinal CT and MRI revealed osteolytic destruction of the T12–L2 vertebrae with paravertebral and psoas abscesses, and chest CT showed diffusely distributed bilateral pulmonary nodules. Based on her epidemiological background, prior TB history, symptoms, and imaging findings, spinal TB with disseminated pulmonary TB was initially suspected. Surgical decompression and abscess drainage were performed, and histopathology demonstrated granulomatous inflammation with caseous necrosis, although acid-fast staining was negative. Despite standard anti-TB therapy, vertebral destruction, paravertebral involvement, psoas abscesses, and pulmonary nodules progressed over 12&#xa0;months. During a second operation, metagenomic next-generation sequencing of pus identified <i>Echinococcus multilocularis</i>, establishing the diagnosis of vertebral and pulmonary AE. Anti-TB therapy was discontinued, and albendazole treatment was initiated. A structured follow-up protocol was established, including clinical assessment every 3–6&#xa0;months, contrast-enhanced MRI of the spine and CT of the chest and abdomen, and routine laboratory monitoring. Follow-up imaging after 3 months showed marked improvement, and the patient’s symptoms substantially resolved by 6 months.</p> Conclusions <p>This case highlights the striking clinical and radiological resemblance between extrahepatic AE and TB, the risk of diagnostic anchoring in endemic settings, and the diagnostic value of mNGS when conventional investigations are inconclusive. The 8-year latency after hepatic surgery underscores the chronic, invasive nature of AE and the need for lifelong surveillance and multidisciplinary management.</p>