Background: Health workers are central to health policymaking. Given health systems’ complex, dynamic and political nature, various forms of ‘hidden power’ are at play as health workers navigate health systems. This study aims to explore the dynamics of power and its sources, and how this shapes policymaking and implementation within the Nigerian health systems context. Methods: The case study was the Global Fund grant in Nigeria, and results are based on an in-depth qualitative study involving 34 semi-structured key informant interviews, board-meeting observations, and documentary analysis conducted in 2014 and 2016. Participants held mid to senior-level positions (e.g. Director, Programme Manager) within organisations involved with Global Fund activities, particularly proposal development and implementation. Data were analysed using thematic analysis in order to gain insight into the power dynamics of health professionals in policy processes. Results: Medical professionals maintained dominance and professional monopoly, thereby controlling policy spaces. The structural and productive power of the biomedical discourse in policy making encourages global actors and the local government’s preference for rapid biomedical models that focus on medications, test kits, and the supply of health services, while neglecting aspects that would help us better understand the poor uptake of these services by those in need. The voices of the repressed groups (e.g non-clinical experts, patients and community based organisations) that better understand barriers to uptake of services are relegated. Conclusion: Professional monopoly theories help illustrate how medical professionals occupy and maintain an elite position in the health system of Nigeria. Structural and agential factors specific to the contexts are key in maintaining this professional monopoly while limiting the opportunities for other health occupations’ rise up the social status ladder.