The application of probiotics as an eco-friendly alternative to antibiotics is an emerging strategy for sustainable aquaculture. In the present study, Rummeliibacillus stabekisii was isolated from the gut of Nile tilapia, and the effects of R. stabekisii on the growth, innate immunity, disease resistance, and gut microbiota of Nile tilapia (Oreochromis niloticus) were investigated. The results showed significantly increased weight gain (WG), feed conversion ratio (FCR), and feed efficiency (FE) in Nile tilapia fed R. stabekisii for 8 weeks compared to those in fish fed a control diet. Intestinal digestive enzymes such as protease, cellulase, and xylanase were also significantly increased in the R. stabekisii-administered groups. Enhanced cumulative survival was exhibited in fish fed R. stabekisii after challenge with Aeromonas hydrophila and Streptococcus iniae. Immune parameters such as the phagocytic activity, respiratory bursts, and superoxide dismutase of head kidney leukocytes; serum lysozyme activity; and expression of the cytokine genes interleukin-1β, tumor necrosis factor-α, transforming growth factor-β, and heat shock protein 70 were significantly elevated in fish fed R. stabekisii. Administration of R. stabekisii considerably increased the abundance of potential probiotics (Bacillus and Lactobacillus spp.) and reduced abundances of potential pathogenic bacteria (Streptococcus and Staphylococcus spp.) in fish intestines. The present study indicated that dietary supplementation with R. stabekisii improved the growth, immunity, disease resistance, and gut microflora of Nile tilapia. This research is the first study reporting that the genus Rummeliibacillus is a potential probiotic in animals, suggesting that R. stabekisii can be used as a feed additive to enhance the growth and health status in tilapia.