This retrospective study sought to determine the safety and effectiveness of flecainide in children with normal hearts and those with congenital heart disease (CHD) or cardiomyopathy (CMO). Baseline and follow-up data at two pediatric cardiology sites were queried (2000–2015); a total of 175 patients (20 with CHD and two with CMO) receiving flecainide were assessed. When comparing patients with CHD to those with normal hearts, patients with CHD were younger at diagnosis (median age 19 days; IQR 3–157.5 days vs normal heart patients median age 21 days; IQR 7–172 days, p = 0.4) and severe cardiac dysfunction was more prevalent (30% in CHD patients vs 8% in normal heart patients, p = 0.009). Treatment duration did not differ between the two groups (CHD patients median duration 52 weeks; IQR 27–91.5 weeks vs normal heart patients median duration 55 weeks; IQR 32–156 weeks, p = 0.5). Cardiac dysfunction resulting in flecainide discontinuation occurred in two patients (1%), one with CHD and one without. Three patients experienced proarrhythmia (2%) and there were no cardiac arrests during follow-up. There was one death in this cohort in a patient with severe CHD and an RSV infection (<1%). Arrhythmia control did not differ between the groups (90% in CHD patients vs 77% in normal heart patients, p = 0.2). Flecainide was well tolerated in this cohort, with fewer than 3% discontinuing medication due to flecainide-associated adverse events. Contrary to adult studies, there was no difference in the incidence of adverse events between patients with normal hearts and patients with CHD. Flecainide is a safe and effective antiarrhythmic medication, even for children with underlying CHD.