In this systematic review and meta-analysis, the effectiveness and safety of 31 acupuncture concerned studies for patients with IBS-D or FD were evaluated. We found that acupuncture can significantly reduce the number of stools per week in IBS-D or FD patients, improve patients’ overall symptoms, improve the total effective rate, decrease the recurrence rate, and reduce the pain level of patients. Based on the results, we believe that acupuncture can improve the quality of life of patients with IBS-D or FD. Although the number of adverse events in the acupuncture group was similar to that in the control group, the majority of adverse events in the acupuncture group were subcutaneous hemorrhage. With such slight adverse events, we have observed that acceptance among patients has not been reduced. Moreover, the withdrawal rate of patients in the acupuncture group was still slightly lower than that in the control group.