Objective:To evaluate the impact of immunisation service integration to nutrition programmes and under 5-year-old outpatient departments of primary health care centres in Rumbek East and Rumbek Centre counties of South Sudan.Design:A retrospective intervention study was conducted in selected primary health care centers (PHCCs).Setting:The study was conducted in 3 primary healthcare centres in Rumbek East county and 3 primary healthcare centres in Rumbek Centre county in Lakes state of South Sudan.Participant:We extracted the data for the uptake of pentavalent vaccine (1st, 2nd and 3rd dose) given to children between 6 weeks old to 23 months old from immunisation records for January to June 2019 before immunisation service integration and July 2019 to December 2019 after immunisation service integration on the District Health Information System 2 (DHIS2) website to estimate the immunisation uptake ratio and drop-out rate.Results:The uptake of the first dose of the pentavalent vaccine improved from 61–96% (p < 0.001) after immunisation service integration into the nutrition programmes of the primary health care centers in Rumbek Centre county. The uptake of the second pentavalent dose improved from 37–69% (p = 0.102) and for the third pentavalent dose from 36–62% (p < 0.001), while the drop-out rate reduced from 57–40% (p < 0.001). While in Rumbek East county, the uptake of the first dose of the pentavalent vaccine improved from 55–77% (p < 0.001) after immunisation service integration into the under 5-year-old pediatric outpatient departments. The uptake of the second dose improved from 36–62% (p < 0.001) and for the third dose from 44–63% (p < 0.001), while the drop-out rate reduced from 40–28% (p < 0.001). Children were 23% more likely (RR: 1.23 [95% CI: 1.01–1.50]) to have been immunised with the first dose of the pentavalent vaccine upon immunisation service integration into the nutrition programmes of primary health care centers 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 rate. Stakeholders of the extended programme on immunisation should focus on the sustainability and scale-up of this intervention as it has high potential to improve childhood immunisation coverage and lower the high rates of vaccine preventable deaths among the children in South Sudan.