Mycoplasma (M.) pneumoniae is a common pathogen causing respiratory infections in children. Pulmonary embolism is a rare complication that may be life-threatening if not diagnosed early and treated promptly. Here, we report the case of an 11-year-old patient with pulmonary embolism associated with M. pneumoniae pneumonia. The patient developed uncorrectable hypoxemia and received venovenous extracorporeal membrane oxygenation treatment. Although the mechanism of thrombosis after M. pneumoniae infection remains unknown, an increase in the cold agglutinin titer indicates that cold agglutinin syndrome might be the mechanism of this pathological change. Finally, the patient was cured with antibiotic and anticoagulant therapies. Patients who have significantly increased C-reactive protein and D-dimer levels and positive cold agglutinin after M. pneumoniae infection should be monitored for the possibility of thrombosis formation.