This systematic review was undertaken with the main aim of assessing the therapeutic effects of herbal medicines in recurrent aphthous stomatitis (RAS). A comprehensive search was performed in PubMed, Scopus, ISI Web of Science, and Google Scholar up to July 2021 to identify randomized clinical trials investigated the effects of herbal medicines on RAS. Thirty-three papers comprising 2,113 patients met the eligibility criteria, of which 30 studies had a high quality based on the Jadad scale. Totally, 22 out of 30 studies which assessed the pain showed that herbal agents significantly decreased the pain compared with the control group or placebo. In 17 out of 25 studies that evaluated ulcer size, herbal agents significantly reduced the size of ulcers compared with the control or placebo groups. In 15 out of 18 studies that assessed the healing time, herbal agents significantly reduced healing time in the intervention groups compared with the placebo or control groups. Few adverse events were reported only in four studies. Findings of the current review indicated medicinal plants and phytochemicals as effective and safe agents that for the treatment of RAS.