Measles remains a major global public health problem. Attainment of high population immunity to measles through vaccination is necessary to control this disease. Children infected with HIV infection often experience secondary measles vaccine failure by 2 years of age, making them susceptible to measles. It is not clear whether HIV-infected children on Highly Active Antiretroviral Treatment (HAART), older than 2 years, have a higher risk of measles than HIV-uninfected children. This retrospective cohort study, guided by the proximate determinants framework, was conducted to compare the risk of measles between HIV-infected children on HAART (exposed) and HIV-uninfected peers (unexposed). The age group with the highest measles susceptibility in the exposed children, which could inform timing for revaccination, was investigated. The role of age at initiation of HAART, low CD4+ count, and undernutrition as predictors of the risk of measles in the exposed children was examined. Univariate, bivariate, and binomial logistic regression analytical procedures were used in data analysis. Results showed no significant difference in the risk of measles between exposed and unexposed children. The age groups 5 to 9 years and 2 to 4 years were the first and second most affected by measles among the exposed children. Undernutrition (stunting) was a significant predictor of measles in exposed children (odds ratio of 4.14, p = 0.02), while age at initiation of HAART and CD4+ count prior to measles exposure were not. The study findings provide evidence to inform vaccination policy and nutrition care for HIV-infected children on HAART in Uganda, so as to reduce their risk of measles illness and mortality, thus contributing to positive social change for the children and the country.