Given Uganda's increasing refugee population, the health financing burden on refugee and host populations is likely to increase because Uganda's integrated health system caters to both populations. We used sexual, reproductive, and maternal health (SRMH) as a lens to assess the utilisation and user cost of health services in Northern Uganda to identify potential gaps in SRMH services and their financing. We conducted a cross-sectional survey among 2,533 refugee and host women and girls in Arua and Kiryandongo districts. We conducted 35 focus group discussions and 131 in-depth interviews with host and South Sudanese refugees, community members, health workers, NGO and governmental actors. Qualitative data were analysed thematically using a framework approach. Quantitative data were analysed using t-test, chi-square tests, multivariate logistical regression, and a two-part model. We found high levels of access to maternal care services among refugee and host communities in Northern Uganda, but lower levels of met need for family planning (FP). Refugees had higher uptake of delivery care than host communities due to better-resourced refugee facilities, but incurred higher costs for delivery kits and food and less for transport due to facilities being closer. FP uptake was low for both groups due to perceived risks, cultural and religious beliefs, and lack of agency for most women. Host communities lack access to essential maternal healthcare services relative to refugees, especially for delivery care. Greater investment is needed to increase the number of host facilities, improve the quality of SRMH services provided, and further enhance delivery care access among host communities. Ongoing funding of delivery kits across all communities is needed and new financing mechanisms should be developed to support non-medical costs for deliveries, which our study found to be substantial in our study. All populations must be engaged in co-designing improved strategies to meet their FP needs.