Objective Sri Lanka has earned a strong reputation for ensuring universally accessible free health and education, gender equality and opportunity for social mobility since her independence. Nevertheless, during the period of protracted civil war, country encountered many challenges to ensure the viability of the social benefits equally throughout the country.

The main purpose of this study was to evaluate the impact of conflict on inequalities in health services provision and health outcomes between direct conflict-affected area and other areas of the country during the conflicts and early phase of the post-conflict period.

Method The main hypothesis of this study was internal conflict negatively affected to the health system in Northern Province and created a health inequality comparing rest of the country. The input process outcome model approach was used for analyzing the inequality in relation to investment to the health, health services provision and health status. Data sources were the Central Bank of Sri Lanka, Department of Census and Statistics, the Ministry of Health, United Nations Development Program and the World Bank.

Results There was a substantial shortage of key health care workers in the direct conflict-affected area during the in-conflict period. However, the government hospital beds density remains higher during the conflicts period and has been increased dramatically in early phase of the post conflict period. Low birth weight prevalence was less and there was no significant difference of major communicable diseases prevalence comparing with the national level.

Although Northern Province showed similar reducing trend of Infant Mortality Rate (IMR) with national level from 1997 to 2016, the Maternal Mortality Ratio (MMR) was significantly higher in Northern Province during the same period.

Conclusion This study reveals even though conflict related health inequalities are unavoidable, it was remained less in Northern Province in Sri Lanka during armed conflict period.