Abstract Background Pediatric ovarian malignant germ cell tumors (POMGCTs) account for the majority of pediatric ovarian malignancies, requiring rigorous surgical oncologic management tailored to pediatric and adolescent populations. In China, due to the lack of dedicated pediatric gynecologic oncology subspecialties, POMGCT patients are treated by either pediatric surgeons or gynecologists, leading to heterogeneous care. However, high-quality multicenter data on cross-specialty surgical disparities and guideline adherence remain scarce. This study aimed to compare surgical management and clinical outcomes between the two specialties and identify determinants of suboptimal guideline adherence. Methods This multicenter retrospective cohort study was conducted at two Chinese institutions from January 2010 to December 2024. Eligible patients were aged ≤ 18 years with histopathologically confirmed POMGCTs who underwent primary surgical treatment, with complete medical records and at least 6 months of follow-up. Patients were categorized into Group A (managed by pediatric surgeons) and Group B (managed by gynecologists) according to the operating surgeon's specialty. Primary outcomes included Children’s Oncology Group (COG)-concordant comprehensive staging completion rate, recurrence-free survival, and overall survival. Between-group comparisons, Kaplan–Meier survival estimation with log-rank tests, and multivariate logistic regression were performed to identify independent risk factors for incomplete staging. Results This 15-year multicenter retrospective study included 82 histologically confirmed POMGCT patients aged ≤ 18 years treated at two Chinese institutions (2010–2024): 60 managed by pediatric surgeons (Group A) and 22 by gynecologists (Group B). Group A had a significantly younger median age (7 vs. 17 years, P P = 0.039) and laparoscopic utilization (45.5% vs. 5.0%, P P P = 0.004), emergency surgery (OR = 4.01, 95% CI: 1.47–10.93, P = 0.006), and incomplete preoperative tumor marker testing (OR = 3.12, 95% CI: 1.15–8.47, P = 0.026). Overall survival was comparable between groups, but suboptimal staging increased recurrence risk. Pediatric surgeons achieved steady improvement in staging compliance over the 15-year period, but still lagged far behind gynecologists. Conclusions While overall survival is similar between specialties, substantial disparities exist in surgical management and COG guideline adherence. Integrating the complementary strengths of pediatric surgery and gynecologic oncology, standardizing clinical workflows, and establishing multidisciplinary teams are critical to optimizing outcomes for Chinese pediatric and adolescent POMGCT patients.