Medication reconciliation (MR), which is widely implemented worldwide, aims to improve patient safety to reduce the medication errors during care transition. Despite its widespread use, MR has not yet been implemented in the Republic of Korea, and its effectiveness has not been studied. We aimed to evaluate the impact of a multidisciplinary MR service in older patients undergoing thoracic and cardiovascular surgery. This is a single-center, prospective, controlled, before-and-after study of adult patients taking at least one chronic oral medication. Depending on the period of each patient’s participation, they will be allocated to an intervention group or control group. Patients in the intervention group will receive multidisciplinary MR, and those in the control group will receive usual care. The primary outcome is to assess the impact of the MR service on medication discrepancies between the best possible medication history and medication orders at care transition. Secondary outcomes include the incidence rate of medication discrepancies at each transition, the discrepancy rate between the sources of information, the impact of MR on medication appropriateness index score, drug-related problems, 30-day mortality, the emergency department visit rate, readmission rate after discharge, the rate and acceptability of pharmacists’ intervention during hospitalization, and patients’ satisfaction.