Recent changes in medical education and assessment led to a focus on occupational competency, and this study investigated the perceptions of Korean medicine doctors (KMDs) on the national licensing examination for KMDs (NLE-KMD). The survey aimed to understand KMDs’ recognition of the current situation, items to improve, and items to emphasize in the future. We conducted the web-based survey from 22 February to 4 March 2022, and 1244 among 23,338 KMDs answered voluntarily. Through this study, we found the importance of competency-related clinical practice and Korean standard classification of disease (KCD), and the presence of a generation gap. KMDs considered clinical practice (clinical tasks and clinical work performance) and the item related to the KCD important. They valued (1) the focus on KCD diseases that are frequently seen in clinical practice and (2) the readjustment and introduction of the clinical skills test. They also emphasized KCD-related knowledge and skills for the assessment and diagnosis of KCD diseases, especially those frequently treated at primary healthcare institutes. We confirmed the generation gap in the subgroup analysis according to the license acquisition period, and the ≤5-year group emphasized clinical practice and the KCD, while the >5-year group stressed traditional KM theory and clinical practice guidelines. These findings could be used to develop the NLE-KMD by setting the direction of Korean medicine education and guiding further research from other perspectives.