Objectives: The Mycobacterium tuberculosis Beijing genotype was first described in 1995 and is now the predominant strain among patients with tuberculosis in many Asian countries. The rapid global spread of the Beijing genotype is receiving increasing attention because it can cause a higher risk of treatment failures. Our objective was to assess the association between the Beijing genotype and unfavourable treatment outcomes of tuberculosis. Methods: We searched for eligible studies through PubMed, Web of Science, Chinese National Knowledge Infrastructure and Wanfang Data. We included cohort studies that evaluated treatment outcomes and Beijing genotype strains. Participants were individuals with active pulmonary tuberculosis. The association between Beijing genotype and the risk of unfavourable treatment outcomes was assessed using the pooled odds ratios (ORs) with corresponding confidence intervals (CIs). Results: In total, 7489 tuberculosis patients were involved in the analysis. Patients infected with the Beijing genotype were more likely to have unfavourable treatment outcomes, with the OR of 2.04 (95% CI 1.52e2.75). The pooled OR was 2.33 (95% CI 1.71e3.16) for recurrence, 2.36 (95% CI 1.69e3.30) for relapse and 2.62 (95% CI 1.90e3.61) for treatment failure, respectively. Subgroup analysis revealed that Beijing genotype was a significant risk factor for unfavourable treatment outcomes in Asians (OR 2.28, 95% CI 1.82e2.86) or in drug-susceptible TB patients (OR 2.11, 95% CI 1.31e3.39). No significant association was observed among non-Asian populations (OR 1.17, 95% CI 0.73e1.86) or patients with multidrug-resistant (MDR) tuberculosis (OR 0.97, 95% CI 0.48e1.94). Conclusions: Our results suggest that Mycobacterium tuberculosis Beijing genotype is associated with an increased risk of unfavourable treatment outcomes, including treatment failure and relapse.