Influenza affects all age groups, but the risk of hospitalization and death due to influenza is strongly age-related and is at its highest among the elderly aged 65 years and older. The objective of this study is to compare the differences in influenza-associated disease burden under three different influenza vaccination strategies—the standard-dose quadrivalent influenza vaccine (QIV), high-dose QIV (HD-QIV), and MF59®-adjuvanted QIV (aQIV)—for the elderly population aged 65 years and older in South Korea. A one-year decision-tree model was developed to compare influenza disease burdens. The input data for the model were obtained from published literature reviews and surveillance data from the Korea Disease Control and Prevention Agency (KDCA). The analysis indicated that aQIV is more effective than QIV, preventing 35,390 influenza cases, 1602 influenza-associated complications, 709 influenza-associated hospitalizations, and 145 influenza-associated deaths annually. Additionally, aQIV, when compared to HD-QIV, also reduced the influenza-associated burden of disease, preventing 7247 influenza cases, 328 influenza-associated complications, 145 influenza-associated hospitalizations, and 30 influenza-associated deaths annually. Switching the vaccination strategy from QIV to aQIV is predicted to reduce the influenza-associated disease burden for the elderly in South Korea. The public health gains from aQIV and HD-QIV are expected to be comparable. Future studies comparing the effectiveness of the vaccines will further inform future vaccination strategies for the elderly in South Korea.