Helicobacter pylori (H. pylori) is a well-established pathogen linked to gastrointestinal disorders, but its role in oral conditions, particularly recurrent aphthous stomatitis (RAS), remains under investigation. This study aimed to evaluate the prevalence of H. pylori in patients with RAS, alongside histopathological analysis of their oral lesions, to provide novel insights into the potential association between this bacterium and oral mucosal diseases. A cross sectional study was conducted on 120 patients with recurrent aphthous ulcers. The study group underwent clinical assessment, bacteriological tests, and histopathological examination of biopsy specimens from affected mucosal areas. The results indicated a significant prevalence (45%) of H. pylori in RAS patients, with a statistically significant correlation between the bacterial presence and severity of ulceration (p < 0.05). Histopathological analysis revealed distinctive inflammatory patterns consistent with bacterial invasion, further substantiating the link. These findings suggest that H. pylori could play a role in the pathogenesis of RAS, opening avenues for targeted therapeutic strategies. The study highlights the novelty of correlating bacteriological findings with histological evidence in RAS, contributing to the growing body of evidence for the oral involvement of H. pylori.