Staphylococcus aureus is an important pathogen that frequently causes clinical disease in children. A wide array of illnesses can be caused by this common pathogen ranging from non-invasive skin infections to severe, life-threatening sepsis. Additionally, as antibacterials have been used to eradicate S. aureus, it has developed resistance to these important therapeutic agents. Methicillin-resistant S. aureus (MRSA) has become an increasing problem in pediatric patients over the past decade. In this review, we discuss the epidemiology, pathogenesis, and treatment options available in treating MRSA infections in children. Specifically, we address the importance of abscess drainage in the treatment of skin and soft tissue infections, the most common clinical manifestation of MRSA infections, and highlight the various agents that are available for treating this common infection. In severe, life-threatening invasive MRSA infections the primary therapeutic option is vancomycin. In cases of MRSA toxic shock syndrome the addition of clindamycin is necessary. In other invasive MRSA infections, such as pneumonia and musculoskeletal infections, the empiric treatment of choice is clindamycin. Finally, newer agents and additional treatment options are discussed.