Background <p>Mycoplasma pneumoniae pneumonia (MPP) is a common community-acquired pneumonia in children, which can uncommonly lead to intracardiac thrombosis. Previous studies have suggested that anticoagulant therapy and thrombolytic therapy were the main treatment options.</p> Case presentation <p>We report the case of a 7-year-old boy with MPP complicated by intracardiac thrombosis and pulmonary embolism. The patient presented with persistent fever, chest pain, and elevated D-dimer levels. The computed tomography angiography (CTA) and echocardiography revealed a thrombus extension from the right inferior pulmonary vein to the left atrium. Considering the risk of thrombus detachment, surgical thrombectomy was performed under cardiopulmonary bypass. Two months follow-up revealed no evidence of new thrombus formation and D-dimer levels normalized.</p> Conclusions <p>In cases of MPP complicated by intracardiac thrombus formation, particularly involving the left heart chambers, surgical thrombectomy may be a viable treatment option. D-dimer served as an important biomarker for both the early detection of thrombosis and the monitoring of treatment efficacy.</p>