Functional dyspepsia (FD) significantly reduces quality of life, and Korean medicine treatment, including herbal medicine, is frequently used in the clinical setting. We aimed to analyze the factors affecting Korean medicine health care (KMHC) use for FD. Data from the Korea Health Panel Survey 2017 were analyzed. Individuals aged > 19 years who were diagnosed with FD and used outpatient care were included. Multiple logistic regression analyses were performed to investigate the association of predisposing, enabling, and need factors with KMHC use for FD, based on Andersen’s behavioral model. The best subsets of factors affecting KMHC use for FD were selected using a stepwise procedure. Participants aged 65 years or older were less likely to use KMHC to treat FD than those aged 19 to 34 years (odds ratio (OR), 0.14; 95% confidence interval (CI), 0.02−0.93). Residents of Busan, Daegu, Ulsan, or Gyeongsang tended to use more KMHC to treat FD than those of Seoul, Gyeonggi, or Incheon (OR, 2.45; 95% CI, 1.02−5.88). Participants with private health insurance were more likely to use KMHC to treat FD than those without private health insurance (OR, 3.41; 95% CI, 1.02−11.42). The prediction model of KMHC use for FD selected sex, age, private health insurance, and stress as the best subset of factors (AUC, 0.709; 95% CI, 0.637−0.781). The results of this study will aid in the decision making of clinicians, researchers, and policymakers.