Since the 1980s treatment techniques for congenital heart disease (ConHD) have gradually evolved. Therefore, actual information on the outcomes, including quality of life is required. Health-related quality of life was assessed long-term in four diagnostic groups of children, who underwent invasive treatment for ConHD between 1990 and 1995. The scores on the TNO-AZL Child Quality of Life Questionnaire (TACQOL) of both children with ConHD and their parents were compared with those of a same-aged reference group. The total sample of ConHD children (n = 113, 8-15 years old) obtained significantly lower mean scores on motor functioning, cognitive functioning, and positive emotional functioning than reference peers, reflecting an experience of poorer functioning. ConHD children, aged 8-11 years, obtained lower mean scores on 5 of the 7 TACQOL scales than reference peers. They also had a lower score on positive emotional functioning than 12- to 15-year-old ConHD children. The total sample of ConHD children obtained lower outcomes compared to their parents on 4 of the 7 TACQOL scales. No significant differences were found in health-related quality of life between ConHD boys and girls, neither between different diagnostic groups. Overall, this sample of recently treated ConHD children showed a worse health-related quality of life compared to reference groups. These findings deserve further attention.