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Abstract Background Mental health care systems in Africa are faced with a high burden of mental disorders. There is need to explore evidence-based, scalable interventions to compliment the “traditional” health care system. Physical activity (PA) can augment the effectiveness of existing programs. However, little is known about the perspectives of health care professionals on PA. Understanding this is key to implementation. Methods This was a qualitative exploratory study based on 13 key informant interviews among experienced health care professionals working at Butabika National Referral and Teaching Hospital, Uganda. Data was analyzed through content thematic analysis. Results Participants reported PA benefits were: improved individual competences and engagement, social reintegration and reduced family and community burden. Self-stigma, lack of community support, lack of infrastructure and equipment, lack of monitoring capacity, human resource challenges and a focus solely on pharmacotherapy were among the most reported barriers to application of PA in management of mental health problems. Conclusion Despite the high level of understanding of PA among health care professionals, PA promotion largely depends on implementation of strategies to deal with community and health systems barriers. Although patients need to be empowered to deal with their individual barriers, greater support and action is needed by policy makers. Public health programs should support PA through community engagement and social re-integration programs. The government should promote a holistic mental health care perspective and provide adequate infrastructural and human resources to support PA in the existing primary and mental health care systems.