Background Hypertension is the single leading risk factor for premature death in Sub-Saharan Africa (SSA). Prevalence is high, but awareness, treatment, and control are low. Community-centred interventions show promise for effective hypertension management, but embedding sustainably such interventions requires a good understanding of the wider context within which they are being introduced. This study aims to conduct a systematic health system assessment exploring the micro (patients/carers), meso (health care workers and facilities), and macro (broader system) contexts in rural Gambia and Kenya. Methods This study will utilise various qualitative approaches. We will conduct focus group discussions with hypertensive patients to map a ‘typical’ patient journey through health systems. We will conduct in-depth interviews with patients, health care workers, and decision-makers to explore their experiences of managing hypertension and assess the capacity and readiness of the health systems to strengthen hypertension management in rural Gambia and Kenya. We will also review national guidelines and policy documents to map the organisation of services and guidance on hypertension diagnosis and control. Thematic analysis approach will be used to analyse data, guided by the cumulative complexity model, and theories of organisational readiness and dissemination of innovations. Expected findings This study will describe the current context for the diagnosis and management of hypertension from the perspective of those involved in seeking (patients), delivering (health care workers) and overseeing (decision-makers) health services in rural Gambia and Kenya. It will juxtapose what should be happening according to health system guidance and what is happening in practice. It will outline the various barriers to and facilitators of hypertension control, as perceived by patients, providers, and decision-makers, and the conditions that would need to be in place for effective and sustainable implementation of a community-centred intervention to improve the diagnosis and management of hypertension in rural settings.