This study aimed to evaluate the use of ozone to treat recurrent aphthous stomatitis (RAS). Consecutive sixty-nine participants with RAS were recruited into this non-randomized double blind, controlled cohort observational study (test group). A control group of 69 RAS patients who matched test group with age and gender was recruited. RAS lesions in test group were exposed to ozone in air for 60 seconds while controls received only air. Ulcer size and pain were recorded for each participant at baseline and daily for 15 days. Ulcer duration was determined by recording the time taken for ulcers to disappear. The main outcome measures were pain due to the ulcer, ulcer size and ulcer duration. 138 RAS participants (69 participants and 69 controls) were analyzed. Ulcer size was reduced starting from the second day in test group and from the fourth day in controls (p ≤ 0.004). Pain levels were reduced starting from the first day in the test group and from the third day in controls (p ≤ 0.001). Ulcer duration, ulcer size after day 2 and pain levels were more reduced in the test group. In conclusion, application of ozone on RAS lesions for 60 seconds reduced pain levels and enhanced ulcers' healing by reducing ulcers' size and duration.