Background: We aimed to study the effectiveness of a “celiac” smartphone application on gastrointestinal symptoms in celiac patients. Methods: In the present randomized controlled clinical trial, 60 celiac patients were randomly assigned to receive education through a smartphone application (n=30) or conventional clinical education (n=30). We assessed the gastrointestinal symptoms using the gastrointestinal symptom rating scale (GSRS) questionnaire at baseline and three months after interventions. The GSRS total score, celiac disease GSRS (CD-GSRS) score, abdominal pain, reflux, diarrhea, constipation, and indigestion scores were calculated. Results: Out of 60 randomized patients, 58 patients completed the study. In comparison to baseline, the mean score of GSRS total score (p=0.04), CD-GSRS score (p=0.001), and indigestion subscore (p<0.001) were significantly decreased in the intervention group. In the control group, compared to baseline, the mean scores of CD-GSRS score (p=0.03) and abdominal pain subscore (p=0.04) were significantly reduced; and the mean score of reflux (p=0.01) subscore was significantly increased. The results of the between-group comparisons showed that although the mean GSRS and CD-GSRS total scores were lower in the intervention group compared with the control group, the differences were not statistically significant. In terms of GSRS subscores, there was a significant difference between the two groups only in the mean score of indigestion (P=0.01).Conclusion: According to the results, smartphone application had a significantly positive effect on indigestion symptoms compared with routine clinic education. However, more large studies with longer duration of the follow-up period are needed to assure this approach Trial registration: The protocol of the study was registered in the Iranian registry of clinical trials (IRCT code: IRCT20170117032004N2). trial registry webpage: : https://www.irct.ir/user/trial/40187/view. Trial registry date: 2019.6.26