Objective <p>This study aimed to investigate the clinical features and management strategies for infective endocarditis(IE) caused by <i>Mycoplasma pneumoniae</i>(<i>M. pneumoniae</i>) in children, in order to enhance understanding of this rare extrapulmonary complication of <i>M. pneumoniae</i> infection and provide clinical insights for its diagnosis and treatment.</p> Methods <p>We retrospectively analyzed the clinical data and management process of a pediatric patient diagnosed with IE who was admitted to our hospital in September 2025.</p> Results <p>A 9-year-old male patient was admitted with initial symptoms of fever and cough and was diagnosed with <i>M. pneumoniae</i> pneumonia. Subsequently, prompted by the detection of a faint blowing murmur on auscultation, transthoracic echocardiography was performed, which revealed a vegetation in the right ventricle. Empirical antibiotic treatment with doxycycline combined with vancomycin and ceftriaxone was initiated. <i>M. pneumoniae</i> was detected in two blood specimens using metagenomic next-generation sequencing (mNGS), while all three conventional blood cultures remained negative. Treatment was subsequently adjusted to doxycycline monotherapy. On hospital day 11, follow-up echocardiography examination showed resolution of the vegetative, with no evidence of thromboembolic events. After discharge, the patient continued oral doxycycline for a total treatment duration of 4 weeks. Follow-up revealed good recovery.</p> Conclusions <p><i>M. pneumoniae</i> pneumonia in children may be complicated by IE. Antimicrobial agents should be guided by regional antimicrobial resistance patterns and resistance gene testing. The addition of anti-inflammatory and anticoagulant therapies should be considered when clinically indicated. mNGS is a valuable diagnostic tool for identifying pathogens in cases of blood culture-negative IE.</p>