Background: Etiological diagnosis of tuberculous pleuritis is challenging owing to the low number of Mycobacterium tuberculosis (MTB) cells in the affected region. Moreover, currently available methods, such as detection of acid-fast bacilli and microbiological cultures, are not always conducive to timely diagnosis and treatment. Objectives: We evaluated the performance of GeneXpert MTB/RIF assay (referred to as “Xpert” hereafter) in detecting MTB in difficult-to-diagnose patients using suspensions of pleural biopsy tissue specimens under direct thoracoscopic guidance. Methods: All suspected patients with pleural effusion who visited Shenyang Tenth People’s Hospital and Shenyang Chest Hospital between 2017 and 2018 were screened. Excluding the confirmed patients, the remaining 160 patients with unexplained pleural effusion underwent local anesthesia, and an intercostal incision of approximately 1.0 cm was made for biopsy. The specimen was used for pathological and etiological examination. The performance of Xpert MTB/RIF test was evaluated for its sensitivity, specificity, and the positive and negative predictive values (PPV and NPV, respectively) against the gold standards, MGIT 960 culture, and a composite reference standard (CRS). Results: The sensitivity and specificity of Xpert were 69.84% and 66.67%, respectively against those of MGIT 960. The PPV and NPV of Xpert were 59.46% and 75.95%, respectively. The sensitivity of Xpert was 70.27% against CRS, which was significantly higher than that of MGIT at 59.26%. The PPV and NPV of Xpert against CRS were 100.0% and 58.75%, respectively. Conclusions: Xpert showed better sensitivity than MGIT in the pleural biopsy and is a potential tool for diagnosing tuberculous pleuritis.