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Abstract Background Hypertension is the most common cardiovascular disease in Nigeria and contributes to a large non-communicable disease burden. Our aim was to implement and evaluate a large-scale hypertension treatment and control program, adapted from the Kaiser Permanent Northern California and World Health Organization HEARTS models, within public primary healthcare centers in the Federal Capital Territory, Nigeria. Methods A type 2 hybrid, interrupted time series design was used to generate novel information on large-scale implementation and effectiveness of a multi-level hypertension control program within 60 primary healthcare centers in the Federal Capital Territory, Nigeria. During the formative phase, baseline qualitative assessments were held with patients, health workers, and administrators to inform implementation package adaptation. The package includes a hypertension patient registry with empanelment, performance and quality reporting, simplified treatment guideline emphasizing fixed-dose combination therapy, reliable access to quality essential medicines and technology, team-based care, and health coaching and home blood pressure monitoring. Strategies to implement and adapt the package were identified based on barriers and facilitators mapped in the formative phase, previous implementation experience, mid-term qualitative evaluation, and ongoing stakeholder and site feedback. The control phase included 11 months of sequential registration of hypertensive patients at participating primary healthcare centers, followed by implementation of the remainder of the package components and evaluation over 37 subsequent, consecutive months of the intervention phase. The formative phase was completed between April 2019 and August 2019, followed by initiation of the control phase in January 2020. The control phase included 11 months (January 2020 to November 2020) of sequential registration and empanelment of hypertensive patients at participating primary healthcare centers. After completion of the control phase in November 2020, the intervention phase commenced in December 2020 and will be completed in December 2023. Discussion This trial will provide robust evidence for implementation and effectiveness of a multi-level implementation package more broadly throughout the Federal Capital Territory, which may inform hypertension systems of care throughout Nigeria and in other low- and middle-income countries. Implementation outcome results will be important to understand what system-, site-, personnel-, and patient-level factors are necessary for successful implementation of this intervention. Trial registration ClinicalTrials.gov NCT04158154 . The trial was prospectively registered on November 8, 2019.