Deep vein thrombosis (DVT) and pulmonary embolism (PE) are relatively rare occurrences in the pediatric population. However, DVT and PE are associated with significant morbidity and mortality to the patient if not promptly diagnosed and treated. We describe the case of a 5-year-old boy that was diagnosed in our emergency department with DVT and PE. The underlying etiology was osteomyelitis of the left tibia caused by community-acquired methicillin-resistant Staphylococcus aureus. The patient had a prolonged hospital course with multiple complications but was eventually discharged in a good condition. In areas with a high prevalence of community-acquired methicillin-resistant S. aureus, it is important for physicians in the emergency department to be aware of the rare, but potentially fatal, complications of infection, including DVT with PE from septic emboli.