Background <p>As probiotics, <i>Bacillus</i> strains may regulate some physiological functions in animals. This study aimed to evaluate whether dietary supplementation with a <i>Bacillus</i>-based probiotic could alleviate gut damage induced by rotavirus (RV) infection in piglets. Twenty-four piglets were randomly assigned into 2 groups fed with the basal diet (<i>n</i> = 16) and the diet containing 10⁹ colony-forming unit <i>Bacillus</i> spores/kg (<i>n</i> = 8). On d&#xa0;8, 8 piglets fed with the diet supplemented with <i>Bacillus</i>-based probiotic and 8 piglets fed with basal diet were orally infused with RV, while the residue piglets had oral gavage of sterile essential medium. The trial duration was 12&#xa0;d.</p> Results <p>RV challenge induced diarrhea, significantly destroyed the morphology of jejunal mucosa (<i>P</i> &lt; 0.05), significantly increased RV-antibody and RV non-structural protein 4 of jejunal mucosa (<i>P</i> &lt; 0.05), significantly impaired antioxidant capacity (including malondialdehyde level, total antioxidant capacity and catalase activity), immunity (such as interleukin 2, interleukin 4 and secreted immunoglobulin A levels), mucins and the mRNA expression of tight-junction-related (such as Zonula occludens 1, occludin) and apoptotic-related (including B-cell lymphoma/leukaemia-2-associated X protein, B cell lymphoma/leukaemia-2, cysteinyl aspartate specific proteinases) genes of jejunal mucosa (<i>P</i> &lt; 0.05), and, to some extents, affected the bacteria community structure and abundance of ileal digesta in piglets. However, <i>Bacillus</i>-based probiotic administration could significantly attenuate the negative effects of RV infection on gut health of piglets (<i>P</i> &lt; 0.05).</p> Conclusions <p>These findings suggested that supplementing <i>Bacillus</i>-based probiotic in the diet could decrease diarrhea rate, and improve gut health in weaned piglets, which was associated with regulating intestinal antioxidant capacity, apoptosis, and microbiota.</p>