Background Published evidence on the drivers of absenteeism among the health workforce is mainly limited to high-income countries. Uganda suffers the highest rate of health workforce absenteeism in Africa, attracting attention but lacking a definitive ameliorative strategy. This study aimed to explore the underlying reasons for absenteeism in the public and private ‘not-for-profit’ health sector in rural Uganda.

Methods We undertook an empirical qualitative study, located within the critical realist paradigm. We used case study methodology as a sampling strategy, and principles of grounded theory for data collection and analysis. Ninety-five healthcare workers were recruited through focus groups and in-depth interviews. The NVivo V.10 software package was used for data management.

Results Healthcare workers’ absenteeism was explained by complex interrelated influences that could be seen to be both external to, and within, an individual’s motivation. External influences dominated in the public sector, especially health system factors, such as delayed or omitted salaries, weak workforce leadership and low financial allocation for workers’ accommodation. On the other hand, low staffing—particularly in the private sector—created work overload and stress. Also, socially constructed influences existed, such as the gendered nature of child and elderly care responsibilities, social class expectations and reported feigned sickness. Individually motivated absenteeism arose from perceptions of an inadequate salary, entitlement to absence, financial pressures heightening a desire to seek supplemental income, and educational opportunities, often without study leave.

Conclusion Health workforce managers and policy makers need to improve governance efficiencies and to seek learning opportunities across different health providers.