Background: Herbal medicines have recently been incorporated into the treatment algorithm for functional dyspepsia (FD). Persian-FACT, a traditional herbal medicine compound, has been used for centuries in Persian medicine to alleviate dyspeptic symptoms. This compound includes anise, fennel, ajwain, and cumin seeds. Objectives: To investigate the efficacy of Persian-FACT as a therapeutic agent for FD. Methods: We conducted an add-on, single-center, double-arm, parallel-group, double-blind, randomized controlled clinical trial at the Imam-Reza Clinic, affiliated with Shiraz University of Medical Sciences in Shiraz, Iran, in 2022. Adults aged 18 to 65 years with a confirmed diagnosis of FD, as referred by a gastroenterologist, were included in the study. After block randomization, participants received sachets containing either Persian-FACT or a placebo (oat) to be taken twice daily for two weeks. The severity of dyspepsia, postprandial distress syndrome (PDS), and epigastric pain syndrome (EPS) (PPI) was assessed using the Gastrointestinal Symptom Rating Scale and the Rome IV questionnaire every week. Results: Thirty-two patients in the Persian-FACT group and twenty-three in the placebo group completed all visits. According to the results of the GEE analysis, the severity of dyspepsia symptoms in the Persian-FACT group was significantly lower than in the placebo group after the intervention (P-value = 0.019). Patients with EPS showed significant improvement from the first week, and those with PDS showed significant improvement after two weeks in the Persian-FACT group compared to the placebo group (P-value = 0.001 vs. P-value = 0.028). Additionally, constipation, gastroesophageal reflux, postprandial fullness, and bloating were significantly reduced with Persian-FACT. Conclusions: Persian-FACT appears to be effective in improving dyspepsia symptoms.