Triester glycerol oxide gel (Protefix® Queisser Pharma, Germany) is a new topical agent that has the property of adherence to the oral mucosa by forming a lipid film which protects against mechanical trauma and may help to reduce oral tissue moisture loss and inflammation. The aim of this clinical trial was to determine the efficacy of a topical TGO gel and to also compare it with triamcinolone acetonide pomade in the treatment of minor recurrent aphthous stomatitis. This study was a randomized, double-blind, placebo-controlled clinical trial and 180 patients with the complaint of minor aphthous ulcers were enrolled in this study. The sociodemographic data and clinical characteristics of the ulcer were collected by questionnaire. Ulcer size and pain level measurements were performed and the efficacy indices for ulcer pain and size were calculated at day 0,2,4,6 by the same investigator. Significant differences were not detected among the demographics and ulcer histories including age, gender, onset of ulcer, mean healing time, family RAS history and ulcer localization between three groups. The pain score in TGO group was found statistically lower at day 2,4, and 6. Efficacy index and improvement rate of TGO group, regarding pain score, was higher than the other two groups at day 2 and 4. The reduction in ulcer size was statistically higher in TGO group than the other two groups at day 4 and 6. Topical application of TGO gel could decrease pain intensity, accelerate ulcer healing without any side effects, utilizing an easy appliable and accessible procedure. Therefore TGO gel could be a well-tolerated, safe, topical therapeutic agent in the clinical practice of RAS treatment.