In the context of recent measles outbreaks, substantial factors associated with measles-mumps-rubella (MMR) unvaccination need to be clarified. This study aimed to identify differential demographic and clinical characteristics between MMR vaccinated and unvaccinated groups. We used a large-linked database to identify children born between 2008 and 2016 by combining data from the Korea Immunization Registry Information System and National Health Information database. The MMR vaccination status was ascertained up to the age of 2 to define MMR vaccinated and unvaccinated groups. We conducted a multivariate logistic regression to estimate odds ratios (ORs) with 95% confidence intervals (CIs) to identify factors associated with MMR unvaccination. Of 3,973,253 children, 75,674 (1.9%) did not receive the MMR vaccine. Compared with the MMR vaccinated group, the underutilization of healthcare resources was more notable in the MMR unvaccinated group (number of outpatient visits (5.73 ± 12.1 vs. 25.8 ± 17.06); days hospitalized (1.69 ± 14.5 vs. 2.32 ± 6.90)). Children were less likely to receive the MMR vaccine if they were born with congenital anomaly (OR 2.12; 95% CI 1.90–2.36), were never admitted to an intensive care unit (1.88; 1.78–1.98), or never visited an emergency room (3.57; 3.53–3.72). There were substantial factors associated with MMR unvaccination, underscoring a need to optimize targeted interventions tailored to the subset of children in South Korea.