Pyomyositis is an infection of the skeletal muscle that involves intramuscular abscess formation. It is typically caused by gram-positive bacteria, especially Staphylococcus aureus. Few cases of Escherichia coli pyomyositis have been reported in immunocompromised adult patients, while none have been reported in children. We present a case of a 4-year-old boy with Down syndrome who developed Escherichia coli pyomyositis. The patient presented to our hospital with a fever and right forearm swelling. The magnetic resonance imaging findings suggested pyomyositis of the right forearm muscle and osteomyelitis of the distal radius. Both the blood and puncture fluid cultures were negative. Cefazolin and vancomycin were administered, and his blood examination results and right forearm swelling improved; however, a slight fever persisted. The multiplex polymerase chain reaction isolated the chuA gene but not the YjaA gene; thus the patient was diagnosed with pyomyositis and osteomyelitis caused by Escherichia coli group D. The cefazolin was substituted with meropenem, and the vancomycin was discontinued. Thereafter, his fever promptly improved, which indicated that the cause of persistent fever was vancomycin drug fever. The patient was discharged after receiving 3 weeks of intravenous antimicrobial therapy, and recovered fully with no long-term sequelae. To the best of our knowledge, this is the first reported case of Escherichia coli pyomyositis in a child. The findings in this case suggest that Escherichia coli should be considered when choosing initial empiric therapy for pyomyositis, especially in children with underlying conditions.