The burden of malaria has persistently been high in Ebonyi state and Nigeria despite long-standing collaborations with international partners with huge and increased amounts of financial investments. We explored the system-wide governance challenges of the Ebonyi State Malaria Elimination Programme (SMEP) and the factors responsible in order to make recommendations for malaria health system strengthening.

We did a qualitative study informed by the health system governance framework by Mikkelsen-Lopez et al and Savedoff’s concept of governance.

Between 18 October 2022 and 8 November 2022, 25 semistructured face-to-face in-depth interviews were conducted in English with purposively selected key stakeholders in the Ebonyi SMEP aged 18 years or older with at least 2 years of involvement in the SMEP and who gave consent.

Data were analysed deductively and the analytical strategy was informed by the framework method for the analysis of qualitative data by Gale et al.

Many system-wide governance challenges of the SMEP were identified including the absence of state’s strategic vision and plans for malaria elimination; very weak primary and secondary healthcare systems; inadequate financial allocation and untimely release of budgeted funds by the state government; lack of human resources for health and very poor mosquito net distribution system. Other challenges were inadequate stakeholders’ participation; poor accountability culture; impaired transparency and corruption and impaired ability to address corruption. The fundamental responsible factors were the lack of state government’s concern for people’s welfare and lack of interest and commitment to the malaria elimination effort, chronic non-employment of staff and lack of human resources in the entire health sector including SMEP, and nepotism and godfatherism.

The system-wide governance challenges and the responsible factors call for changing the ‘business as usual’ and refocusing on strengthening malaria health system governance in addressing the persisting malaria health problems in Ebonyi state (and Nigeria).