Pediatric cardiac catheterization requires unconsciousness and immobilization through general anesthesia or sedation. This study aimed to compare the occurrence of severe complications in pediatric diagnostic cardiac catheterization for ventricular septal defect between general anesthesia and sedation performed under similar institutional environments. Using the Japanese Diagnosis Procedure Combination database, we retrospectively identified pediatric patients (aged <2 years) who underwent diagnostic cardiac catheterization for ventricular septal defect between July 2010 and March 2019. The composite outcome was the occurrence of severe complications, including catecholamine use and intensive care unit admission, within seven days after catheterization. Overlap weighting based on propensity scores was used to adjust for patient- and hospital-level confounding factors. We identified 3159 patients from 87 hospitals, including 930 under general anesthesia and 2229 under sedation. The patient- and hospital-level baseline characteristics differed between the groups. After adjustment, the proportion of patients with severe complications was significantly higher in the general anesthesia group than in the sedation group (2.4% vs. 0.6%; risk difference, 1.8% [95% confidence interval, 0.93-2.6%]). Severe complications occurred more frequently in the general anesthesia group than in the sedation group. Further research on anesthetic methods is necessary to assess the safety and accuracy of pediatric diagnostic cardiac catheterization.