Background: Recurrent aphthous stomatitis (RAS) is a highly prevalent oral mucosal disease. The management of RAS is quite challenging, and as yet, there is no definitive cure. The present systematic review and meta-analysis assessed the efficacy of a single application of topical doxycycline for the management of RAS. Methods: A comprehensive online search of PubMed, Scopus, Embase, and Web of Science databases was conducted to identify all relevant studies published up to March 31, 2019. All randomized clinical trials that assessed the efficacy of a single application of topical doxycycline in the management of RAS were included. Primary outcome measures were pain scores and/or healing time, while secondary outcomes included the associated side effects. RevMan 5.3 software was used for data analysis. Results: Five clinical trials fulfilled the eligibility criteria, three of which were included in the meta-analysis. All of the included studies found doxycycline effective in alleviating signs and symptoms of RAS. The results of the pooled 3 studies revealed a statistically significant decrease in the healing time in favor of the doxycycline group as compared to the control groups (I 2 = 51%; MD:-1.77, 95% CI: − 2.11, − 1.42, P <0.00001); however, the results showed no significant differences between doxycycline and control groups with regard to pain reduction (I 2 = 96%; MD:-1.28, 95% CI: − 2.83, 0.27; P = 0.11). Conclusion: Although still inconclusive, the available evidence suggests that a single application of topical doxycycline might be effective for reducing signs and symptoms of RAS. However, owing to the limited number of the included studies, further well-designed clinical trials with adequate sample sizes are required to discern the clinical efficacy of topical doxycycline in patients with RAS.