While operational efficiency has been evaluated in adult interventional and surgical specialties, limited data exist regarding the prediction of case complexity in the pediatric and congenital electrophysiology (EP) laboratory. To identify pre-procedural variables that predict prolonged case durations among pediatric and adult congenital patients presenting for diagnostic EP study and catheter ablation. A retrospective cross-sectional study was performed of all EP studies performed at Boston Children’s Hospital between 1/1/2015-1/1/2020 including pediatric and adult congenital heart disease patients of all ages. The primary outcome was case duration ≥180 minutes. Univariate and multivariate analyses were performed for the primary outcome using logistic regression, with a sub-analysis repeated for pediatric patients <20 years of age. During the 5-year period, 1025 patients underwent EP study and 292 (28.5%) had a case duration ≥180 minutes. Factors associated with the primary outcome on multivariate analysis were: age ≥20 years at EP study (OR 1.95, 95% CI 1.24-3.07, p 0.004), arrhythmia diagnosis of premature ventricular contractions/ventricular tachycardia (PVC/VT, OR 3.70, 95% CI 2.10-6.55, p <0.001), Fontan (OR 3.74, 95% CI 1.69-8.30, p=0.001) or Mustard/Senning physiology (OR 4.13, 95% CI 1.48-11.60, p=0.007), and the presence of non-cardiac comorbidities (OR 2.47, 95% CI 1.29-4.73, p 0.006). Restricting the analysis to pediatric patients <20 years old, factors associated with the primary outcome on multivariate analysis were an arrhythmia diagnosis of PVC/VT (OR 3.04, 95% CI 1.64-5.63, p <0.001), Fontan physiology (OR 3.13, 95% CI 1.10-8.92, p 0.033), non-cardiac comorbidities (OR 4.32, 95% CI 2.07-9.01, p <0.001), and prior ablation (OR 1.58, 95% CI 1.03-2.41, p 0.035). Intra-atrial reentrant tachycardia was not associated with prolonged case duration in either multivariate model. A weighted risk score using factors identified on multivariate analyses correctly classified procedures with prolonged case duration with reasonable accuracy (c-statistic 0.70). Age-dependent anatomic, electrophysiologic, and comorbid factors are associated with prolonged case duration in the pediatric and congenital EP laboratory. Applying a simple risk score using pre-procedural variables can discriminate cases with and without prolonged duration, and may aid in efficient procedural scheduling practices.