Abstract Aims Advances in surgical techniques allow an increasing number of children with congenital heart disease (CHD) to reach adulthood. As patients grow older, atrial fibrillation (AF) is evolving into a major clinical concern and can be difficult to manage medically. Primary AF catheter ablation may, therefore, have a role in this setting but few reports have evaluated its efficacy in CHD patients. Methods and results We retrospectively reviewed 58 consecutive patients [median age 51, interquartile range (IQR) 44–63 years, 57% male] with AF (45% paroxysmal) who underwent 122 ablation procedures in our tertiary centre in the last decade. The majority had CHD of moderate or severe complexity (57%, Bethesda Class 2 or 3) with a dilated left atrium (LA) (81%) and/or right atrium (86%). At 1-year from the first ablation, 32.8% of patients remained in sinus rhythm. Multiple procedures were required in 35 (60%) patients. Freedom from AF at 1-year after the 2nd and 3rd ablation was 40.9% and 36.5%, respectively. Multivariable predictors of AF recurrence were underlying anatomic complexity [hazard ratio (HR) in Bethesda 3 1.98, P = 0.006], type of AF (HR for persistent 1.87, P = 0.004), and indexed LA dimensions (HR for cm2/m2 1.06, P = 0.03). Conclusion While ablation may be a valid option for the treatment of AF in CHD patients, multiple procedures are likely to be required. Early referral and careful patient selection are essential to optimize the results of AF ablation, achieving a low rate of recurrence. Further studies are needed to validate our prognostic model and guide clinical practice.