OBJECTIVE: To evaluate the impact of immunisation service integration to nutrition programmes and under 5-year-old paediatric outpatient departments of primary healthcare centres in Rumbek East and Rumbek Centre counties of South Sudan. DESIGN: Retrospective intervention study. SETTING: Three primary healthcare centres in Rumbek East county and three primary healthcare centres in Rumbek Centre county of Lakes state in South Sudan. PARTICIPANT: We extracted the data for the uptake of pentavalent vaccine (first, second and third dose) given to children aged between 6 weeks and 23 months from immunisation records for January-June 2019 before immunisation service integration and July-December 2019 after immunisation service integration from the District Health Information System 2 website to estimate the immunisation uptake ratios and drop-out rates. RESULTS: The uptake of the first dose of the pentavalent vaccine improved from 61% to 96% (p<0.001) after immunisation service integration into the nutrition programmes of the primary healthcare centres in Rumbek Centre county. The uptake of the second pentavalent dose improved from 37% to 69% (p<0.001) and for the third pentavalent dose from 36% to 62% (p<0.001), while the drop-out rate reduced from 57% to 40% (p<0.001). While in Rumbek East county, the uptake of the first dose of the pentavalent vaccine improved from 55% to 77% (p<0.001) after immunisation service integration into the under 5-year-old paediatric outpatient departments. The uptake of the second dose improved from 36% to 62% (p<0.001) and for the third dose from 44% to 63% (p<0.001), while the drop-out rate reduced from 40% to 28% (p<0.001). Children were 23% more likely (RR 1.23, 95% CI 1.12 to 1.36, p<0.001) to be immunised with the first dose of the pentavalent vaccine on immunisation service integration into the nutrition programmes of primary healthcare centres of Rumbek Centre county in comparison to integration into under 5-year-old outpatient departments of Rumbek East county. CONCLUSION: Integration of immunisation service delivery to nutrition sites and children's outpatient departments improved the immunisation coverage and decreased drop-out rates in the Rumbek East and Rumbek Centre counties of South Sudan. This evidence of positive impact should encourage the stakeholders of the Expanded Programme on Immunisation to focus on the sustainability and scale-up of this intervention to other counties in South Sudan, as logistically as possible.