BACKGROUND: The vast majority of refugees are hosted in low and middle income countries (LMICs), which are already struggling to finance and achieve universal health coverage for their own populations. While there is mounting evidence of barriers to health care access facing refugees, there is more limited evidence on equity in access to and affordability of care across refugee and host populations. The objective of this study was to examine equity in terms of health needs, service utilisation, and health care payments both within and between South Sudanese refugees and hosts communities (Ugandan nationals), in two districts of Uganda. METHODS: Participants were recruited from host and refugee villages from Arua and Kiryandongo districts. Twenty host villages and 20 refugee villages were randomly selected from each district, and 30 households were sampled from each village, with a target sample size of 2400 households. The survey measured condition incidence, health care seeking and health care expenditure outcomes related to acute and chronic illness and maternal care. Equity was assessed descriptively in relation to household consumption expenditure quintiles, and using concentration indices and Kakwani indices (for expenditure outcomes). We also measured the incidence of catastrophic health expenditure- payments for healthcare and impoverishment effects of expenditure across wealth quintiles. RESULTS: There was higher health need for acute and chronic conditions in wealthier groups, while maternal care need was greater among poorer groups for refugees and hosts. Service coverage for acute, chronic and antenatal care was similar among hosts and refugee communities. However, lower levels of delivery care access for hosts remain. Although maternal care services are now largely affordable in Uganda among the studied communities, and service access is generally pro-poor, the costs of acute and chronic care can be substantial and regressive and are largely responsible for catastrophic expenditures, with service access benefiting wealthier groups. CONCLUSIONS: Efforts are needed to enhance access among the poorest for acute and chronic care and reduce associated out-of-pocket payments and their impoverishing effects. Further research examining cost drivers and potential financing arrangements to offset these will be important.