The objective of this study was to explore the key elements of Korean medicine (KM) treatment for idiopathic short stature (ISS) by analyzing the strengths, weaknesses, opportunities, and threats (SWOT). This was a qualitative study of interviews with 7 KM doctors who had at least 3 years of experience in KM treatment for ISS. Based on the content, a SWOT and a cross-SWOT analysis were conducted. A SWOT of KM treatment for ISS was derived as follows: Strengths included the additional positive health promotion effects and fewer possibilities of adverse effects. Weaknesses included insufficient long-term evidence on the effect and safety and difficulty in predicting prognosis for ISS treatment in KM. Opportunities included a growing interest in height growth in general and the need for parental involvement in children height growth. Threats included the limited use of diagnostic devices and relatively high medical costs due to non-coverage by national health insurance. This study suggests that the safety and clinical effectiveness evidence of KM treatment for height growth should be guaranteed through well-designed large-scale long-term studies. Various strategies are needed to promote the use of diagnostic and evaluation devices for ISS treatment in KM clinical settings.