A 12-year-old Chinese boy was admitted with dyspnea after exercise. Based on his clinical features, echocardiography tests, and family history, he was diagnosed with Noonan syndrome (NS) combined with noncompaction of the ventricular myocardium (NVM). Noonan syndrome (NS) is a common syndrome, but to the best of our knowledge, our case is the first reported case of NS combined with NVM. In our case, the detected mutated genes may be inherited and unreported genes caused NS or NVM. Our research may enrich our knowledge about NS and contribute to furthering our understanding of the pathogenesis and treatment. In summary, we present a unique case of NS combined with NVM.