Staphylococcus aureus (S. aureus) is a Gram-positive bacterium that causes infections ranging from mild superficial cases to more severe, potentially fatal conditions. Many photosensitisers used in photodynamic therapy are more effective against superficial infections due to limitations in treating deeper tissue infections. Recently, attention to this bacterium has increased due to the emergence of multidrug-resistant strains, which complicate antibiotic treatment. As a result, alternative therapies, such as antimicrobial photodynamic therapy (PDT), have emerged as promising options for treating non-systemic infections. PDT combines a photosensitiser (PS) with light and oxygen to generate free radicals that destroy bacterial structures. This systematic review evaluates the effectiveness of PDT delivered via different types of hydrogels in treating wounds, burns, and contamination by S. aureus. Following PRISMA 2020 guidelines, a bibliographic search was conducted in PubMed, Web of Science, and Scopus databases, including articles published in English between 2013 and 2024. Seven relevant studies were included, demonstrating evidence of PDT use against S. aureus in in vitro and in vivo studies. We concluded that PDT can effectively complement antimicrobial therapy in the healing of wounds and burns. The effectiveness of this technique depends on the PS used, the type of hydrogel, and the lesion location. However, further in vivo studies are needed to confirm the safety and efficacy of PDT delivered via hydrogels.