Background Major achievements in congenital heart disease (CHD) treatment over the past 20 years have altered the course and prognosis of CHD. Improvement of quality of life (QoL) is now a major goal of CHD treatment. Objective To assess the QoL in children after cardiac surgery for CHD. Methods A cross-sectional study was performed in children aged 2 to 18 years. The case group had 20 children with a history of corrective heart surgery in the 12 months prior to the study. The control group had 20 healthy children, age-matched to the case group. The QoL of both groups was assessed by Pediatric Quality of Life Inventory (PedsQL) Generic Core Scales. The same post-operative children were also assessed with the PedsQL Cardiac Module. Data were analyzed using T-test with P < 0.05 as the level of significance. Results This study recruited 40 subjects: 20 post-operative and 20 healthy children. PedsQL Generic Core Scales assessment showed significant differences between groups in the physical function parameter of QoL (P<0.05) in children aged 13-18 years, but there were no significant differences in the social, emotional, and school function parameters. In children aged 2-12 years, there were no significant differences in physical, social, emotional, or school parameters. The PedsQL Cardiac Module assessment revealed that 35% of post-operative children was at risk for physical appearance problems, 80% was at risk for anxiety problems, 40% was at risk for cognitive problems, and 80% was at risk for communication problems. Conclusion Thirteen to 18-year-old children with non complex CHD have poorer physical function than healthy children. Post operative children are at risk for physical appearance, anxiety, cognitive, and communication problems.