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Abstract Background The Democratic Republic of Congo (DRC) has one of the highest numbers of un and under-vaccinated children as well as number of refugees and internally displaced persons (IDPs) in the world. This study aims to determine and compare the proportion and characteristics of zero-dose (ZD) and under-vaccinated (UV) children among refugees and IDPs in the DRC, as well as the reasons for incomplete vaccination schedules. Methods Data from a rolling vaccination coverage survey conducted from September 10, 2022, to July 03, 2023, among refugees and IDPs in 12 provinces of the DRC. ZD was defined as a child aged 12–23 months who had not received any dose of pentavalent vaccine DTP-Hib-Hep B (by card or recall) and UV as a child who had not received the third dose of pentavalent vaccine. The proportions of non and under-vaccination and the associated factors using a logistic regression model are presented for ZD and UV children. The reasons for non-vaccination of these children are described using the WHO-Immunization behavioral and social-drivers-conceptual framework and compared using Pearson’s Chi2 test. Results Of 692 children aged 12 to 23 months included in the analysis, 9.3% (95% CI: 7.2–11.7%) were ZD and 40.9% (95% CI: 95%: 37.2–44.6%) UV. The Penta1/Penta3 drop-out rate was 34.9%. After adjustment, ZD children had a significant history of home or road birth. And UV children were significantly associated with mothers/caregivers being under 40, uneducated, farmers, ranchers, employed, rural residents, as well as with home or road births. Reasons linked to people’s perceptions and feelings were cited much more often for ZD (50.0%) than for UV (38.3%). Those related to social reasons were cited much more often by ZD (40.6%) than by UV (35.7%). Reasons related to “programmatic and practical issues” were cited less for ZD (90.5%) than for UV (97.1%). Conclusions ZD and UV children represent significant proportions in refugee and IDPs sites in the DRC. However, the proportion of ZD is less than for the entire country, while the proportion of UV is comparable, reflected in a very high drop-out rate. Similarly to studies in the general population in DRC, the reasons for ZD children were mainly linked to challenges in caregiver motivation to vaccinate, while for UV children, they were more often linked to pro-grammatic and practical problems of the health system.