Objective To investigate the clinical features, diagnosis, treatment, and prognosis of the rare complication of infectious endocarditis (IE) in children with Mycoplasma pneumoniae pneumonia (MPP), aiming to enhance clinicians' understanding and facilitate early diagnosis of this condition. Methods A retrospective analysis was conducted on the clinical data of 5 children with MPP complicated by IE admitted to our hospital from January 2023 to November 2024. The analysis included clinical manifestations, laboratory tests, imaging findings, etiological test results, treatment, and follow-up information. Results The median age of onset was 9 years (5-9.5) years, with a male-to-female ratio of 3:2. All patients presented with fever and cough; only one exhibited concomitant subxiphoid pain. Median duration of fever was 12 (9.5-15) days, and vegetations were detected on echocardiography at a median of 10 (8-12) days after disease onset. Elevated D-dimer levels 5.09 (4.35-7.9) μg/mL and fibrin degradation products 10.56 (7.2-24.71) mg/L indicated marked hypercoagulability, while increased IL-6 55.45 (33.02-95.56) pg/mL and lactate dehydrogenase 746 (568.45-838.9) U/L suggested significant systemic inflammation and tissue injury. All children tested positive for MP nucleic acid in respiratory specimens; however, only one had MP DNA detected in blood via metagenomic next-generation sequencing (mNGS). All underwent surgical excision of vegetations, with histopathological examination confirming the diagnosis of IE. Postoperatively, all received antimicrobial therapy and anticoagulation. Among them, three patients with confirmed pulmonary embolism continued long-term anticoagulation for 1-6 months post-discharge. Follow-up echocardiography revealed no vegetation recurrence, and no patient reported symptoms such as dyspnea, chest pain, or wheezing during the monitoring period. Conclusion MPP-related IE presents with nonspecific and often insidious early manifestations, posing challenges for timely diagnosis. In pediatric patients with MPP and evidence of hypercoagulability, routine echocardiographic screening is strongly recommended to enable early detection of IE and prevent diagnostic delays. With prompt diagnosis and comprehensive management, the prognosis is favorable.