Flecainide is frequently used for treatment of cardiac arrhythmias in children. Due to concerns regarding increased mortality, there has been hesitancy to use flecainide in children with congenital heart disease (CHD) or cardiomyopathy (CM). The objective of this study was to describe trends in use of flecainide in children with CHD or CM and assess its association with cardiac arrest or death. Data from 42 children’s hospitals contained in the PHIS database (2004–2011) were analyzed. All patients with CHD or CM receiving anti-arrhythmic therapy for supraventricular arrhythmias were reviewed. Trends in flecainide use were analyzed, and the incidence of cardiac arrest or death was compared to patients receiving other anti-arrhythmics. There were 3,544 pts with CHD or CM who received anti-arrhythmic therapy (median age 73 days). Flecainide was administered in 229 pts (6.5 %). There was a trend toward increased use of flecainide in this population, increasing from 4.6 % in 2004 to 8.7 % in 2011 (p = 0.07). The incidence of cardiac arrest in patients with CHD or CM receiving flecainide was 3.0 % with an overall mortality of 4.3 %. The mortality was 2.9 % in pts with CM and nobody with single ventricle physiology died. Based on multivariable analysis, when compared to pts with CHD or CM receiving other anti-arrhythmics, there was no difference in the incidence of cardiac arrest (p = 0.31) or death (p = 0.28). Flecainide use in children with CHD or CM has increased in recent years. The incidence of cardiac arrest or death with flecainide administration in this cohort appears comparable to other anti-arrhythmic agents.