Objective To explore the predictive value of vegetation size on the prognosis of pediatric infective endocarditis (IE). Methods A total of 27 children diagnosed with IE who were admitted to Kunming Children's Hospital from January 2014 to June 2024 were included. The good prognosis group comprised 10 cases, while the bad prognosis group comprised 17 cases. The receiver operating characteristic (ROC) curve, restricted cubic spline model, and decision curve analysis were utilized to assess the predictive value of vegetation size on the prognosis of pediatric IE. Results There were statistically significant differences in vegetation size, hemoglobin, platelet count, and prothrombin time between the two groups (P < 0.05). The ROC curve demonstrated that vegetation size had a high predictive accuracy for the prognosis of pediatric IE (AUC = 0.841, 95% CI: 0.775-0.924). Decision curve analysis indicated that vegetation size held substantial clinical value for predicting the prognosis of pediatric IE. The restricted cubic spline analysis revealed a linear dose-response relationship between vegetation size and prognosis of pediatric IE (nonlinear test, P = 0.084). Conclusion Significant differences were observed in vegetation size, hemoglobin, platelet count, and prothrombin time between different prognosis of pediatric IE. Limited evidence indicates that vegetation size is a critical factor in predicting the prognosis of pediatric IE. However, studies with larger sample sizes are needed to confirm the accuracy of these conclusions.