The herbal medicine Yukgunja-tang has been widely used for the treatment of functional dyspepsia (FD) in the clinical setting of East Asian traditional medicine. This paper presents a protocol for a randomized, assessor-blind, controlled, multicenter, three-arm parallel clinical trial comparing the effectiveness, safety, and cost-effectiveness of Yukgunja-tang with Pyeongwi-san and usual care. A total of 140 participants with Rome IV-diagnosed FD will be randomly assigned to either the Yukgunja-tang (n = 56), Pyeongwi-san (n = 56), or usual care (n = 28) groups. All participants will be educated on dietary guidelines for FD patients. Participants in the Yukgunja-tang and Pyeongwi-san groups will take investigational products for 6 weeks. All participants will be assessed for clinical parameters at weeks 0, 3, 6, 9, and 24. The primary outcome will be measured on the total dyspepsia symptom scale, and the secondary outcome will include the single dyspepsia symptom scale, overall treatment effect, the visual analog scale for dyspepsia, FD-related quality of life, hospital anxiety and depression scale, EuroQol-5 dimension, pattern identification, and serum levels of acyl-ghrelin and deacyl-ghrelin. Adverse events and laboratory tests will be monitored for safety assessment. The results will provide evidence of the effectiveness, safety, and cost-effectiveness of Yukgunja-tang in the treatment of FD.