Despite the significant attention paid to inequities in national development, they persist in Ghana. Social services such as health, education, water and sanitation exhibit differentials depending on where citizens live. Decentralisation has often been proposed as a means of making these services more equitable. Examining the case of the health sector, this paper contends that the nature of health sector decentralisation coupled with funding inequities among districts sustains health inequities in Ghana's decentralised units. In-depth interviews are conducted in four districts in the Northern and Greater Accra regions in Ghana, alongside national level officers within the decentralised and health system. As part of the analysis, tapes were transcribed and coded, and data generated were analysed for themes and patterns. Findings reveal that funding inequalities, as well as the concurrent existence of multiple strands of decentralisation in the health sector, result in persistence of inequities. If decentralisation is to positively impact on inequities in the health system, there must be clarity and a streamlining of the cooperation and coordination between and at all levels of the health sector and the districts.