The protracted war in South Sudan has led to severe humanitarian crisis with high level of malnutrition and disruption of the health systems with continuous displacement of the population and low immunization coverage predisposing the population to vaccine preventable diseases. The study aimed at evaluating the effect of integrating immunization services with already established nutrition services on immunization coverage in resource-constrained humanitarian response.A community and health facility based interventional study involving integration of immunization into nutrition services in two Outpatient Therapeutic Program(OTP)centers in Bentiu PoC between January-December 2017. The main hypothesis was that inclusion of immunization services during nutrition services both at the OTP and community outreaches be an effective strategy for reducing missed opportunity for immunizing all eligible children accessing nutrition services. Data analyzed using STATA version 15 and bivariate analysis using logistic regression was conducted to identify predictor of missed vaccinations.Integration of immunization into the nutrition services through the OTP centres increased the number of children immunized with various antigens and the dropout rate was much lower and statistically significant among children who received immunization at the OTP centers than those in the Primary Health Care Centers (PHC Centers) in the study sites. Children who were vaccinated at the OTP centre in sector 2 were 45% less likely to miss vaccination than those vaccinated at the PHCC (OR: 0.45; 95%CI:0.36- 0.55), p<0.05 while those vaccinated at the OTP sector in sector 5 were 27% less likely to miss vaccination than those vaccinated at the PHCC (OR: 0.27; 95%CI: 0.20 -0.35) p<0.05).This study indicated that immunization coverage improved effectively with integration with nutrition services as a model of an integrated immunization programme for child health in line with the Integrated Management of Childhood Illnesses (IMCI) and the Global Immunization Vision and Strategy (GIV).