Abstract Background While the significance of good governance is recognised within health systems research, its role in health system reform is underexplored. This research focuses on the establishment of new decentralised regional health structures in Ireland in the period 2018-2023, examining how aspects of governance impacted the decentralisation reform process, from policy design through to implementation. Methods The research applied a qualitative, multi-method approach involving analysis of official documents relevant to the regional decentralisation process, and 12 semi-structured interviews with key informants from across the health sector. The research applies the TAPIC framework for health governance as its analytic framework and the data is analysed using thematic analysis. Results Deficiencies in accountability arrangements, poor transparency within the system and vis-à-vis external stakeholders, and a lack of clarity of roles and responsibilities for various process and key decisions related to the reform were identified as undermining progress at various stages of Ireland’s decentralisation reform process. An underlying distrust between key institutional actors was identified. These findings are grounded in complex social, cultural, and political and institutional developments in Ireland’s history. Also of note is the interwovenness of the five TAPIC domains and the importance of engaging with the complexity and relationality intrinsic to health system reform processes to achieve the aim(s) of the reform in question. Conclusions Large scale health system reform is a complex process and its governance presents distinct challenges and opportunities for stakeholders. To understand and address these, critical analysis of the historical context surrounding the policy reform and the institutional relationships at its core are needed. Key messages • Governance plays a crucial if overlooked role in health systems reform. Effective governance arrangements are central to the successful design and implementation of reform initiatives. • Ensuring a strong link between policy design and implementation processes is crucial to the success of health systems reform.