Introduction: Measles elimination interventions in South Sudan have relied on mass campaigns due to reoccurring humanitarian crisis over decades. This paper examines the effects of targeted measles vaccinations on efforts at eliminating measles in the country. Methods: Time trend and an analytical cross-sectional design were applied on South Sudan Measles case-based surveillance dataset 2011-2015. Logistic regression of IgM positive cases against vaccination status and adjusted for age and unknown vaccination status were used to determine the likelihood of reduced risk of measles at 95% CI. Results: Routine immunization, follow-up and outbreak response coverage for measles vaccination over the period were sub-optimal. Even though the proportion of confirmed measles cases among vaccinated population was irregular ranging 14.2% to 61.9% within the period reviewed, measles vaccination generally reduced the risk of the disease in the population by 30% (odds 0.7, 95% CI 0.4, 1.0) from 2011-2015. A trend analysis showed that the likelihood of reduction of measles burden varied per year, but a higher reduction of risk was observed in 2015 (odds 0.05 (95% CI <0.01, 0.35) preceded by follow-up campaigns. Adjusting for age and unknown vaccination status, there were no statistically significant difference for the trends of odds, however the significant decrease in odds in 2015 (OR 0.01 (95% CI [0.01, 0.35]) R 2 0.45) is due to a unit change in age. Conclusions: Targeted measles outbreak vaccinations generally reduce the burden of measles however the extent of reduction is more reflected in a year following a mass measles campaign as compared to outbreak response vaccination. Thus measles follow-up campaigns are necessary for sustained measles control and elimination.