Patients with Behçet’s disease often use complementary and alternative medicine for treating their symptoms, and herbal medicine is one of the options. This systematic review provides updated clinical evidence of the effectiveness of herbal medicine for the treatment of Behçet’s disease (BD). We searched eleven electronic databases from inception to March 2020. All randomized controlled trials (RCTs) or quasi-RCTs of BD treatment with herbal medicine decoctions were included. We used the Cochrane Handbook for Systematic Reviews of Interventions to assess the risk of bias and the grading of recommendations assessment, development and evaluation (GRADE) approach to assess the certainty of evidence (CoE). Albatross plot was also used to present the direction of effect observed. Eight studies were included. The risk of bias was unclear or low. The methodological quality was low or very low. Seven RCTs showed significant effects of herbal medicine on the total response rate (Risk ratio, RR 1.26, 95% CI 1.09 to 1.45, seven studies, very low CoE). Four RCTs showed favorable effects of herbal medicine on the erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) level compared with drug therapy. Herbal medicine favorably affected the ESR (MD −5.56, 95% CI −9.99 to −1.12, p = 0.01, I2 = 96%, five studies, very low CoE). However, herbal medicine did not have a superior effect on CRP. Two RCTs reported that herbal medicine significantly decreased the recurrence rate after three months of follow-up (RR 0.23, 95% CI 0.09 to 0.63, two studies, low CoE). Our findings suggest that herbal medicine is effective in treating BD. However, the included studies had a poor methodological quality and some limitations. Well-designed clinical trials with large sample sizes are needed.