Background <p>Noncommunicable diseases (NCDs), including hypertension and diabetes, account for approximately 27% of all deaths in Kenya, with 26% of adults having elevated blood pressure. Despite devolution of health services to county governments in 2013, financing for NCD management at the primary health care (PHC) level remains weak. This study examines financial determinants shaping hypertension and diabetes care in PHC facilities within a devolved county health system in rural Kisumu County, Kenya.</p> Methods <p>We conducted a convergent parallel mixed-methods cross-sectional study in seven public PHC facilities in Seme Sub-County, providing new facility-level evidence on how the interaction between devolution’s financing architecture, facility-level financial autonomy constraints, and resource allocation mechanisms shapes chronic disease care effectiveness in rural Kenya. Quantitative data were collected via structured questionnaires and retrospective document review of financial records (January–August 2024). Qualitative data were gathered through key informant interviews (<i>n</i> = 7) with facility in-charges exploring planning, budgeting, and resource allocation. Descriptive statistics were produced in STATA v16; qualitative data were analyzed thematically in R.</p> Results <p>All seven facilities prepared annual workplans and budgets, but none achieved comprehensive NCD-specific planning (workplan + budget + dedicated NCD budget line). Funding sources were narrow: 71.4% (<i>n</i> = 5) of the facilities depended on NHIF reimbursements and donor support, while only 28.6% (<i>n</i> = 2) received direct county funding; 57.1% (<i>n</i> = 4) of the facilities relied on only two funding streams. Although all facilities held bank accounts, none had formal financial autonomy and expenditures required county-level approval, typically taking 3–4 weeks (57.1%, <i>n</i> = 4) to over two months (28.6%, <i>n</i> = 2). Combined with unreliable central supplies, this lack of autonomy meant facilities could not procure locally when stockouts occurred; consequently 85.7% (<i>n</i> = 6) of the facilities reported frequent medication stockouts. Facility in-charges attributed these failures to inadequate, unpredictable funding and centralized approval processes that prevented timely local procurement.</p> Conclusions <p>Rural PHC facilities operate under structural governance failures in Kenya’s devolved health financing system that systematically undermine effective NCD care. The centralization of financial authority at county level, absence of ring-fenced NCD budgets, and misalignment between planning processes and resource allocation represent system-level policy contradictions rather than facility-level operational deficiencies. Addressing these governance failures requires not only increased funding but constitutional fiscal decision-space for facilities, mandatory NCD budget protection, and reformed disbursement mechanisms essential for equitable chronic care under Kenya’s UHC agenda. The sustainability of chronic care depends fundamentally on facility decision space, not only on funding volume. These findings are transferable to other Kenyan counties under the same devolved framework and to decentralized health systems in sub-Saharan Africa facing similar tensions between fiscal accountability and operational autonomy for chronic disease management.</p>