Background There is limited population-based research on benign ovarian surgery in children and how practice patterns have changed over time. Oophorectomy may carry detrimental effects on long-term health outcomes, and it is unclear if there are factors associated with ovary-conserving surgery and how often subsequent surgeries are required. Methods Population-based retrospective cohort study including all children under 18 years undergoing benign ovarian surgery from 2003 – 2022 in Ontario, Canada, using administrative healthcare data capturing all hospitalization, emergency department, and procedural records at an individual level. Trends in laparoscopy, surgery at pediatric institutions, and ovarian-conserving surgery were described. Multivariable log-binomial regression analysis identified patient, surgeon, and institution factors associated with ovarian-conserving surgery. Cumulative probability of undergoing subsequent ovarian surgery up to 20 years following initial surgery was calculated using Kaplan–Meier estimates. Results A total of 3,452 children underwent benign ovarian surgery between 2003 and 2022 in Ontario, with 2,827 (81.9%) ovarian-conserving surgeries and 625 (18.1%) oophorectomies performed. Over the study period, there was an increase in laparoscopy (63% to 83%), surgeries at pediatric hospitals (32% to 56%), and ovarian-conserving surgeries (80% to 87%), evaluated by the Cochrane-Armitage test (p < 0.0001). Multivariable log-binomial regression analysis identified several factors associated with ovarian-conserving surgery: laparoscopy (RR 1.40, 95% CI 1.33–1.47, p< 0.0001), female surgeons (RR 1.04; 95% CI 1.01–1.07, p = 0.0057), and non-gynecologist (RR 1.04; 95% CI 1.01–1.08, p = 0.0133). Ovarian-conserving surgeries were less likely in rural patients (RR 0.93, 95% CI 0.88–0.98, p = 0.009), and in younger children aged < 5 (RR 0.84, 95% CI 0.75–0.94, p = 0.0023) and aged 5–9 years (RR 0.85, 95% CI 0.75–0.96, p = 0.0066) compared to children aged 15–17 years. Probability of subsequent ovarian surgery was more likely after ovarian-conserving surgery (cumulative incidence 0.17, 95% CI 0.13–0.22) compared to oophorectomy (cumulative incidence 0.08, 95% CI 0.05–0.11), continuing to trend upward for both. Conclusions Pediatric ovarian surgery in Ontario is evolving, with rising rates of laparoscopy, use of pediatric hospitals and ovarian-conserving surgeries. There are several patient/surgeon factors associated with ovarian-conserving surgery. Risk of subsequent ovarian surgery continued to rise 20 years after initial surgery for all individuals, highlighting importance of ovarian conservation where possible.