This paper describes the development of and lessons learned in implementing the Primary Health Care Access Program (PHCAP) in the Northern Territory. The implementation of the PHCAP is a major Aboriginal health policy reform. PHCAP provides an opportunity for Aboriginal people to gain access to properly resourced comprehensive primary health care (PHC) services. PHCAP is described in its unique funding model that attempts to address tensions within the federal governance system. In this paper we argue that access to PHC services is a key determinant of health and that funding of PHC services has been inadequate and inequitable throughout the Northern Territory. The implementation of PHCAP is reforming the existing health system and leading to the establishment of new PHC services. We analyse the barriers encountered in this process. The PHCAP funding model is analysed for its adequacy and design strength to address federal relations. We consider issues of workforce shortage that will limit our capacity to implement the program and the need for effective regional PHC support services. We conclude that the basic funding model within PHCAP - a grant payment plus access to the Medicare Benefits Schedule and Pharmaceutical Benefits Scheme - is the best possible way to fund comprehensive PHC at the present time, and call for bipartisan party commitment to fully realise the potential of this program to address Aboriginal health inequalities.