In response to escalating antibiotic resistance, Methicillin-resistant Staphylococcus aureus (MRSA) infections, especially chronic intracellular cases, pose a persistent challenge. Phage therapy offers a promising alternative, targeting intracellular MRSA effectively. This review explores phage therapy's mechanisms, efficacy, challenges, and future prospects, with a focus on transduction risks. The review details phage therapy's intricate mechanisms against MRSA, highlighting dynamic phage-bacterial interactions within host cells. Evidence and case studies underscore transduction risks, including genetic element transfer and antibiotic resistance acquisition. Studies demonstrating phage therapy's efficacy against intracellular MRSA stress the need for tailored strategies and innovative approaches for enhanced phage access and efficacy within cells. Challenges like phage resistance and cell penetration limitations are examined, with proposed solutions to improve intracellular phage activity. Cutting-edge technologies such as whole-genome sequencing and single-cell analysis are discussed for monitoring and controlling transduction events. Collaboration among researchers, healthcare professionals, and regulators is emphasized to establish robust guidelines and address biosecurity concerns in phage therapy applications.