Introduction: According to the nature of heart diseases and the use of cardiopulmonary bypass, transient or permanent neurologic complications may arise during or after pediatric cardiac surgery. The aim of this study was to evaluate the incidence of acute neurologic complications in postoperative cardiac surgery period in children with congenital heart diseases (CHD) undergoing cardiac surgery. Materials and Methods: In this study, all patients with cardiovascular disease (including CHD and other cardiovascular diseases) had been operated (open or closed) in the Children’s Medical Center, Tehran, Iran, were evaluated for a year between July 2014 and July 2015. Those who had died during hospital stay or surgery, patients with incomplete information in their medical records, and children who had not been operated because of CHD were excluded. Of the 435 patients surveyed, 364 patients were enrolled in this study. Acute neurologic complications and related findings in brain CT scan were investigated. Results: The age range for patients was between 5 days to 15 years old, of whom 64 (17.6%) patients were under 2 months, 131 (36%) patients were between 2 months to 1 year, and 169 (46.6%) patients were over one year. Thirty-three patients (9.06%) were identified with acute neurological complications after heart surgery, including seizures, movement disorders, loss of consciousness, visual disturbances, headache, and hydrocephalus. Conclusion: Improving the implementation of the cardiopulmonary bypass protocols and using neural monitoring for ischemia and bleeding as well as arterial filter during surgery can reduce the incidence of neurological complications after pediatric cardiac surgery.