Diagnosing prosthetic valve infective endocarditis in children is challenging. Transthoracic and transesophageal echocardiography can yield false-negative results. Data are lacking in paediatric multimodality imaging in prosthetic valve infective endocarditis. We present two children with repaired CHD where initial echocardiogram was non-diagnostic, while CT angiogram and 18F-fluorodeoxyglucose positron emission tomography in combination with CT angiography, respectively, confirmed the diagnosis of endocarditis affecting clinical management.