INTRODUCTION: Functional dyspepsia (FD) is a functional gastrointestinal disorder characterized by persistent upper dyspeptic symptoms without organic lesions. There is no standard therapy for FD. Yukgunja-tang (YGJT) is an herbal medicine used for treating upper gastrointestinal symptoms in Asia. Studies on the effect of YGJT on FD have been conducted. However, the results were inconsistent. In medicine, traditional Korean medicine, FD patients are classified into bladder body (BB) or gallbladder body (GB) subtypes by the shape and angle of their faces. Each subtype may have different characteristics, physiology, and pathology of the same disease. YGJT is more effective for patients with BB subtype. The three-dimensional facial shape diagnostic system (3-FSDS) was shown to be effective in diagnosing BB or GB subtypes. This study aimed to investigate the effect of YGJT on FD patients classified using the 3-FSDS. MATERIALS AND METHODS: The current study was a placebo-controlled, double-blinded, randomized, two-center trial. Eligible patients were diagnosed with either BB or GB FD subtype using the 3-FSDS. Ninety-six participants (48 BB and 48 GB subtypes) were randomly allocated to treatment or control groups in a 2:1 ratio. YGJT or placebo was administered for eight weeks. The primary outcome was assessed using the total dyspepsia symptom scale (TDS), while the secondary outcomes were assessed using the single dyspepsia symptom scale (SDS), proportion of responders, visual analog scale, Nepean dyspepsia index, functional dyspepsia-related quality of life, and spleen qi deficiency questionnaire. RESULTS AND DISCUSSION: The result of TDS showed the superior effect of YGJT on BB over GB subtype. The subgroup analysis of TDS and SDS scores showed the superior effect of YGJT over placebo. Other outcome variables did not show any significant differences between groups. CONCLUSION: YGJT may be considered for FD patients diagnosed with BB subtype using 3-FSDS.