Background: We aimed to assess the efficacy and safety of a herbal preparation STW 5-II containing extracts from bitter candy tuft, matricaria flower, peppermint leaves, caraway, licorice root and lemon balm for the treatment of patients with functional dyspepsia. Methods: 120 patients with functional dyspepsia were randomly assigned to 1 of 4 treatment groups. Each patient received the treatment for three consecutive 4-week treatment blocks. The first two treatment blocks were fixed. For the third treatment period, medication was based upon the investigator’s judgement of symptom improvement during the preceding treatment period. In patients without adequate control of symptoms, the treatment was switched, or if symptoms were controlled, the treatment was continued. The primary outcome measure was the improvement of a standardized gastrointestinal symptom score (GIS). Findings: During the first 4 weeks, the GIS significantly decreased in subjects on active treatment compared to the placebo (p < 0.001). During the second 4-week period, symptoms further improved in subjects who continued on active treatment or who switched to the active treatment (p < 0.001), while symptoms deteriorated in subjects who switched to placebo. After 8 weeks 43.3% on active treatment and 3.3% on placebo reported complete relief of symptoms. (p < 0.001 vs. placebo). Conclusion: In patients with functional dyspepsia, the herbal preparation tested improved dyspeptic symptoms significantly better than placebo.