Background: Recurrent aphthous stomatitis (RAS) is a major oral health problem, where its etiopathogenesis is not well understood. Accordingly, its therapy whether topical or systemic can induce clearance, but the relapse rate is high. Objective: To use 100% topical pumpkin seed oil in RAS as it has many actions as anti-inflammatory and antioxidant effects. Patients and Methods: This single, blind, clinical, therapeutic trial was conducted in the Department of Dermatology-Baghdad Teaching Hospital, Baghdad, Iraq, during February 2015-August 2016. Twenty-five patients with RAS were included in this work. After full history and clinical examination, the clinical diagnosis was established. Oral clinical manifestation index score (OCMI) was carried out before, during and after stopping therapy to assess the different parameters of this score. 100% Topical pumpkin seed oil was given two times daily for 3 months during which short term assessment for each patient was done by using OCMI before, after 4 days and after 8 days of therapy in addition to assessing the mean size of largest diameter of ulcers in each visit to evaluate the therapeutic efficacy of the therapy, while long term assessment of the OCMI was done every month for 3 months after starting of the therapy to evaluate the prophylactic effect of the therapy. After 3 months, pumpkin seed oil was stopped and assessment of OCMI was done monthly for another 3 months to evaluate the remission action of pumpkin seed oil. Results: Twenty-five patients were included in this study: 15 (60%) males and 10 (40%) females. While their ages ranged from 9 -60 (27.48 ± 11.97) years. The mean of OCMI before pumpkin seed oil therapy was ranged from 9 -15 (12.96 ± 1.42), while after the therapy the mean started to decline to lower level within 4 days of therapy and was statistically significant (p < 0.0001) and continued to decline significantly till the end of third month of therapy (p < 0.0001). The percent reduction was 79.30% after 4 days of therapy and 94.38% after 8 days of therapy. After stopping therapy, the mean of OCMI started to increase, but it is remained statistically highly significant (p < 0.0001) at the end of third months after stopping therapy when it is compared with baseline mean of OCMI. Conclusion: Pumpkin seed oil had an effective therapeutic and prophylactic action against RAS, in addition, it induced remission for at least 3 months after stopping therapy. No local or systemic side effects were observed during the course of therapy.