Background Cotrimoxazole and isoniazid preventive therapy (CPT, IPT) have been shown to be efficacious therapies for the prevention of opportunistic infections and tuberculosis (TB) among people living with human immunodeficiency virus (HIV). Despite governments' efforts to translate World Health Organization recommendations into practice, implementation remains challenging. This review aimed to explore and compare CPT and IPT with respect to similarities and differences of barriers identified across high TB/HIV burden countries. A secondary objective was to identify facilitators for implementing both preventive therapies. Methods We searched MEDLINE, Web of Science and SCOPUS databases for peer-reviewed literature published before September 2020. We extracted and synthesized our findings using Maxqda software. We applied framework synthesis in conjunction with metasummary to compare both therapies with respect to similarities and differences of barriers identified across seven health system components (in line with the modified WHO's Framework for action). Protocol registration: PROSPERO (CRD42019137778). Findings We identified four hundred and eighty-two papers, of which we included forty for review. Although most barrier themes were identical for both preventive therapies, we identified seven intervention-specific themes. Like for CPT, barriers identified for IPT were most frequently classified as 'service delivery-related barriers' and 'patient & community-related barriers'. 'Health provider-related barriers' played an important role for implementing IPT. Most facilitators identified referred to health system strengthening activities. Conclusions For researchers with limited working experience in high TB/HIV burden countries, this review can provide valuable insights about barriers that may arise at different levels of the health system. For policymakers in high TB/HIV burden countries, this review offers strategies for improving the delivery of IPT (or any newer therapy regimen) for the prevention of TB. Based on our findings, we suggest initial and continuous stakeholder involvement, focusing on the efficient use and reinforcement of existing resources for health.