BACKGROUND: Decentralisation is argued to promote community participation, accountability, technical efficiency, and equity in the management of resources, and has been a recurring theme in health system reforms for several decades. In 2010, Kenya passed a new constitution that introduced 47 semi-autonomous county governments, with substantial transfer of responsibility for health service delivery from the central government to these counties. Focusing on two key elements of the health system, Human Resources for Health (HRH) and Essential Medicines and Medical Supplies (EMMS) management, we analysed the early implementation experiences of this major governance reform at county level. METHODS: We employed a qualitative case study design, focusing on Kilifi County, and adapted the decision space framework developed by Bossert et al., to guide our inquiry and analysis. Data were collected through document reviews, key informant interviews, and participant and non-participant observations between December 2012 and December 2014. RESULTS: As with other county level functions, HRH and EMMS management functions were rapidly transferred to counties before appropriate county-level structures and adequate capacity to undertake these functions were in place. For HRH, this led to major disruptions in staff salary payments, political interference with HRH management functions and confusion over HRH management roles. There was also lack of clarity over specific roles and responsibilities at county and national government, and of key players at each level. Subsequently health worker strikes and mass resignations were witnessed. With EMMS, significant delays in procurement led to long stock-outs of essential drugs in health facilities. However, when the county finally managed to procure drugs, health facilities reported a better order fill-rate compared to the period prior to devolution. CONCLUSION: The devolved government system in Kenya has significantly increased county level decision-space for HRH and EMMS management functions. However, harnessing the full potential benefits of this increased autonomy requires targeted interventions to clarify the roles and responsibilities of different actors at all levels of the new system, and to build capacity of the counties to undertake certain specific HRH and EMMS management tasks. Capacity considerations should always be central when designing health sector decentralisation policies.