Aim Total colonic aganglionosis (TCA) is a severe form of Hirschsprung’s disease (HD) associated with a high morbidity. This study assessed long-term functional outcome and quality of life (QoL) of patients with TCA in a national consecutive cohort. Methods Surgical and demographic characteristics in the medical records of all patients (n = 53) diagnosed with TCA between 1995 and 2015 were reviewed. Functional outcome of all nonsyndromal patients, aged ≥ 4 years (n = 35), was assessed using a questionnaire and in medical records. Generic and disease-specific QoL were assessed using standardized validated questionnaires. Results Of 35 patients eligible for follow-up, 18 (51%) responded to the questionnaires. They were aged 4–19 years. A Duhamel procedure was performed in 67% of these patients and a Rehbein procedure was performed in 33%. In the questionnaire, 65% of the patients reported constipation, 47% faecal incontinence and 53% soiling. Moreover, 18% of patients used bowel management (flushing or laxatives) and 29% had an adapted diet only. Children and adolescents with TCA had worse perception of their general health and were more limited by bodily pain and discomfort compared with healthy peers. Their quality of life is influenced most by frequent complaints of diarrhoea and other physical symptoms. Conclusion Children and adolescents with TCA report lower health-related QoL compared with healthy peers, especially in the physical domain. We suggest standardized follow-up and prospective longitudinal future research on functionality and QoL of these patients.