Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of severe respiratory infections, particularly in patients with chronic pulmonary diseases, and its treatment often necessitates prolonged use of broad-spectrum or potent anti-MRSA antibiotics. While these therapies are essential for infection control, they frequently disrupt gut microbiota, leading to dysbiosis and gastrointestinal complications such as antibiotic-associated diarrhea and Clostridioides difficile infection. Increasing evidence indicates that antibiotic-induced gut dysbiosis may also influence respiratory immunity through the gut–lung axis, potentially affecting pulmonary inflammation and infection outcomes. Probiotics have emerged as a potential adjunctive strategy to mitigate antibiotic-related gastrointestinal adverse effects by restoring microbial balance, enhancing intestinal barrier integrity, and modulating host immune responses. This narrative review examines current preclinical, indirect clinical, and limited clinical evidence regarding the role of probiotics in alleviating gastrointestinal side effects of antibiotic therapy in MRSA-related respiratory infections and explores their suggestive immunomodulatory effects on pulmonary health via gut–lung immune interactions. Experimental and observational studies indicate that probiotic-mediated restoration of gut microbiota and microbial metabolites, particularly short-chain fatty acids, may exert systemic immunoregulatory effects extending to the lungs. However, direct, high-quality clinical evidence specifically supporting probiotic use in MRSA pneumonia remains limited and preliminary. Overall, probiotics represent a microbiome-centered supportive approach with biological plausibility but incomplete clinical validation for improving gastrointestinal tolerance to antibiotic therapy and supporting immune homeostasis in MRSA respiratory infections. Further well-designed, MRSA-specific clinical trials incorporating microbiome and immunological endpoints are required before definitive clinical recommendations can be made.