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Deep vein thrombosis (DVT) is a rare disease in pediatric patients. We report a pediatric patient who developed DVT in association with methicillin-resistant Staphylococcus aureus (MRSA) bacteremia complicated with septic arthritis, osteomyelitis, and myositis extensively. It is crucial to consider musculoskeletal infection associated with DVT in any child who presents with severe swollen limbs and limitations of motion. Prompt antibiotic and anticoagulant treatments should be initiated to reduce the risk of fatal complications.