Purpose Single-site laparoscopic percutaneous extraperitoneal ligation (SLPEL) for pediatric inguinal hernia has gained popularity worldwide. However, complications associated with extraperitoneal knotting are not rare. This study evaluated the effectiveness of a modified SLPEL (M-SLPEL) to decrease adverse events associated with ligation knotting by comparing it with two other methods: classical SLPEL (C-SLPEL) and intracorporeal purse-string suturing (IPS). Methods A multicenter retrospective comparative study was conducted among 5523 pediatric inguinal hernia patients. Cases were divided into three groups according to the surgical procedure: the M-SLPEL, C-SLPEL, and IPS groups. Data describing the clinical characteristics, operative time, and complications were collected. Results All procedures were performed uneventfully. There were no significant differences in the age at operation (mean 2.62 ± 1.38 years). The operative time was shorter in the M-SLPEL group both for unilateral hernias (12.5 ± 1.8 min in C-SLPEL, 11.7 ± 1.3 min in M-SLPEL, and 17.6 ± 2.9 min in IPS) and for bilateral hernias (15.1 ± 2.1 min, 14.6 ± 1.7 min, and 23.9 ± 2.3 min, respectively). The overall incidence of adverse events in the inguinal region was 0% for M-SLPEL, 2.2% for C-SLPEL, and 0.5% for IPS. All patients were followed up for 12–93 months (mean 54 months). Recurrence occurred in 8 cases in the C-SLPEL group, 1 case in the M-SLPEL group, and 8 cases in the IPS group, with no significance between groups. No scrotal hematoma, testicular atrophy, or iatrogenic cryptorchidism occurred in any group. Conclusion The M-SLPEL procedure has time-consumption efficiency equivalent to that of C-SLPEL and even fewer adverse events in the inguinal region than IPS and C-SLPEL.