Stress in dogs during breeding or transport can trigger substantial physiological and behavioral disturbances, including anxiety, appetite reduction, immune suppression, gut microbial imbalance, and even mortality. While pharmacological treatments are widely used for stress management, few specifically target gut health. This study investigates the effectiveness of a new probiotic strain, Enterococcus faecium Kimate-X, in reducing transport-induced stress and supporting intestinal microbiota in dogs, offering a non-drug-based alternative. In vitro experiments revealed that Kimate-X enhanced superoxide dismutase (SOD) and catalase (CAT) activities while decreasing malondialdehyde (MDA) and tumor necrosis factor-α (TNF-α) levels in RAW 264.7 macrophages. In vivo, dogs receiving Kimate-X supplementation exhibited lower cortisol levels after transport, indicating reduced stress. Metagenomic analyses demonstrated increased gut microbial diversity and elevated short-chain fatty acids (acetate, propionate, and butyrate) in feces. These results suggest that Kimate-X alleviates transport stress in dogs by modulating gut microbiota, supporting the use of probiotics as a viable strategy for stress mitigation.