This paper uses the National Health Accounts (NHA) framework to investigate the differences in the Northern and Southern regions? patterns of health financial flows, and the implication for health outcomes in the region. The study is based on the federal structure of governance in the country which has shaped both health financing and delivery in Nigeria with all the three tiers of government involved in health care delivery organisation, management and financing. The paper found that health care financing in both the North and South of Nigeria is heavily dependent on household and the proportional share by the household is disproportionately against the North because of the higher poverty incidence in the north. With lower health financial flows in the North, the health outcomes in this region remain relatively significantly poor. This raises equity concerns as those who are least able to pay are made to bear the greater burden. The current overburden of the household requires exploration of alternative financing mechanisms by the government. Public facilities are the main users of the health funds in the country accounting for an average of more than 60% of all funds spent in the health sector. The dominance of the public providers is more prominent in the North, where more than 71% of health services are spent in public facilities, while both the public and private facilities in the South receive approximately equal share of the health spending in the region. Policy implications of our findings means that the fragile health insurance scheme in the country should be strengthened through broadening of its coverage to both formal and informal sectors of the economy. In addition, government should bring health issue to the fore by increasing resource allocation to health.