Noncompaction of the ventricular myocardium (NVM) is exceedingly rare and associated with a high morbidity and mortality. This pathology has been associated with other congenital heart diseases (CHDs). The efficacy of surgical treatment of patients with NVM and other CHDs is largely unknown. The aim of the present study was to describe surgical outcomes of 16 patients. Between April 2009 and October 2011, 16 patients with NVM and CHD were admitted to our hospital. Through a clinical chart review, we analyzed results of surgical treatment of NVM with other CHDs retrospectively. The median age was 3.9 years (range 2 m-11 y). The follow-up time was 23.93 months (range 3 m-36 m). Two patients (12.5%) died after the surgery, the remaining patients (87.5%) had an uneventful postoperative course. An additional patient died due to sudden death three months after surgery. Two patients developed recurrent heart failure after surgery. Congestive heart failure, severe arrhythmias, and the range of NVM may be risk factors for death. At 6 months after the operation, the NYHA functional class was significantly improved (2.38 ± 0.89 vs. 1.62 ± 0.65, p = 0.009). The cardiothoracic ratio was significantly reduced when compared to before the operation (p < 0.001). Surgery in patients with NVM and other CHDs can be effective in relieving heart failure, improving heart function, and decreasing heart size.