Health and health service access in Zambian prisons are in a state of ‘chronic emergency’. This study aimed to identify major structural barriers to strengthening the prison health systems. A case-based analysis drew on key informant interviews (n = 7), memos generated during workshops (n = 4) document review and investigator experience. Structural determinants were defined as national or macro-level contextual and material factors directly or indirectly influencing prison health services. The analysis revealed that despite an favourable legal framework, four major and intersecting structural factors undermined the Zambian prison health system. Lack of health financing was a central and underlying challenge. Weak health governance due to an undermanned prisons health directorate impeded planning, inter-sectoral coordination, and recruitment and retention of human resources for health. Outdated prison infrastructure simultaneously contributed to high rates of preventable disease related to overcrowding and lack of basic hygiene. These findings flag the need for policy and administrative reform to establish strong mechanisms for domestic prison health financing and enable proactive prison health governance, planning and coordination.