The World Health Organization (WHO) recommends tuberculosis preventive treatment (TPT) in people with HIV (PWH), yet implementation remains poor, especially in rural communities. We examined factors influencing TPT initiation in PWH on antiretroviral therapy (ART) in rural South Africa using the Promoting Action on Research Implementation in Health Services (PARiHS) framework to identify contextual factors and facilitation strategies to successfully implement TPT. Patient and clinical factors were extracted from medical records at two primary healthcare clinics (PHCs). Among 455 TPT eligible indivdiuals, only 263 (57.8%) initiated TPT. Patient-level characteristics (older age and symptoms of fever or weight loss) were significantly associated with TPT initiation in bivariate analysis, but PHC was the only independent correlate of TPT initiation (aOR: 2.24; 95% CI: 1.49-3.38). Clinic-level factors are crucial targets for implementing TPT to reduce the burden of HIV-associated TB. Gaps in knowledge of HCW, staff shortages, and non-integrated HIV/TB services were identified barriers to TPT implementation. Evidence-based strategies for facilitating TPT implementation that might be under-prioritized include ongoing reprioritization, expanding training for primary care providers, and quality improvement strategies (organisational changes, multidisciplinary teams, and monitoring and feedback). Addressing contextual barriers through these facilitation strategies may improve future TPT implementation in this setting.