ObjectivesTo explore the facilitators and barriers that affected the design and implementation of the first 3 years of Sudan’s largest health programme on female genital mutilation (FGM).DesignWe used a qualitative case study guided by the Consolidated Framework for Implementation Research to conduct in-depth interviews with programme managers and for thematic data analysis.SettingAbout 14 million girls and women in Sudan are affected by FGM, which is mainly performed by midwives (77%). Since 2016, Sudan has received substantial donor funding to develop and implement the largest global health programme to stop midwives’ involvement and improve the quality of FGM prevention and care services.ParticipantsEight Sudanese and two international programme managers representing governmental, international and national organisations and donor agencies participated in interviews. Their job positions required detailed involvement in planning, implementing and evaluating diverse health interventions in the areas of governance, building knowledge and skills of health workers, strengthening accountability, monitoring and evaluation and creating an enabling environment.ResultsRespondents identified funding availability and comprehensive plans, integration of FGM-related interventions within existing priority health intervention packages and presence of an evaluation and feedback culture within international organisations as implementation facilitators. The barriers were low health system functionality, low inter-organisational coordination culture, power asymmetries in decision-making during planning and implementation of nationally-funded and internationally-funded interventions, and non-supportive attitudes among health workers.ConclusionUnderstanding the factors affecting planning and implementation of Sudan’s health programme addressing FGM may potentially mitigate barriers and improve results. Interventions which change midwives’ supportive values and attitudes towards FGM, strengthen health system function and increase intersectoral and multisectoral coordination including equitable decision-making among relevant actors, may be needed to address the reported barriers. The impact of these interventions on the scale, effectiveness and sustainability of the health sector response merits further study.