Gastric ulcer is one of the most common gastrointestinal tract diseases with a higher extent in male patients to. Selenium nanoparticles (SeNPs) possess therapeutic benefits, including antimicrobial, antioxidant, anti-inflammatory, and anti-ulcerative agents. The study aimed to investigate the modulatory effect of yeast-mediated SeNPs on gastric ulcers and microbiota dysbiosis in a rat model. Twenty-four rats were randomly divided into four groups. Both the control and SeNPs-only groups received distilled water orally, and after 1 h, they received 2 % carboxymethyl cellulose (CMC). The ulcer model and SeNPs-treated groups received 99 % ethanol (5 ml/kg orally) for ulcer induction, followed by 2 % CMC after one hour. The SeNPs-treated group got SeNPs (60 mg/kg) suspended in 2 % CMC. We measured ulcer markers (ulcer index and gastric juice pH and volume and stomach tissue oxidative stress markers (malondialdehyde (MDA), glutathione (GSH), nitric oxide (NO), and catalase (CAT)), in addition to histopathological examination of gastric tissues stained with three different satins: hematoxylin-eosin (H&E), periodic acid-Schiff (PAS), and Masson's trichrome stains (many-color dye), and microbiological analysis of freshly collected fecal sample. SeNPs treatment significantly decreased gastric volume, ulcer index, malondialdehyde, and increased glutathione levels. A macroscopic examination of the treated stomach revealed decreased ulcer lesion numbers. Furthermore, histopathological examination showed that SeNPs treatment repaired ulcerative gastric tissue through the regeneration of epithelial cells and reduction in damaged areas and collagen fibers. In the treated group, microbiological analysis of rat feces showed a significant increase in Leuconostoc pseudomesenteroides, Escherichia coli, and Enterococcus faecium counts. This research suggests that SeNPs exhibit anti-ulcer activity and can accelerate ulcer healing via their antioxidant action. They also have a modulatory effect on gut microbiota dysbiosis associated with gastric ulcers. This is the first research studying the impact of safe yeast-mediated SeNPs on rat's gastric ulcer and gut microbiota.