Objectives To validate the Hospital Anxiety and Depression Scale (HADS) and the 10-item Perceived Stress Scale (PSS-10) for use in clinical studies of recurrent aphthous stomatitis (RAS) and to provide cross-sectional assessment of anxiety, depressive, and distress symptoms and perceived stress in patients with RAS. Methods The validity and reliability of the HADS and PSS-10 were evaluated in 120 individuals with RAS through confirmatory factor analysis and calculation of Cronbach's alpha and omega coefficients. The prevalence of comorbid anxiety, depression, distress, and moderate-to-high perceived stress, and their association with demographics and clinical factors were assessed through cutoff scores of the HADS and PSS-10 and bivariate analyses, respectively. Results A bi-factor model, with all items loading onto general factor with two group factors, provides the best fit to the HADS and PSS-10 data of this RAS cohort. While omega values suggested adequate reliability of total score of both scales, relatively low ranges of coefficient omega hierarchical limit utility of their subscale scores. The prevalence of anxiety, depression, distress, and moderate-to-high perceived stress was 42.5%, 18.33%, 28.33%, and 71.67%, respectively. Ethnicity, alcohol consumption, disease comorbidities, clinical type of RAS, ulcer size, pain, and RAS disease activity were found to be associated with negative psychological symptoms. Conclusion The HADS and PSS-10 are valid and reliable as general scales of psychological distress and stress in patients with RAS. Significant mental burden among RAS patients makes the use of these validated instruments a sensible and prudent practice for psychological assessment of this patient group.