Pacing indications in children are clearly defined, but whether an epicardial (EPI) or an endocardial (ENDO) pacemaker performs better remains to be elucidated. This systematic review and meta-analysis aimed to directly compare the incidence of pacemaker (PM) lead-related complications, mortality, hemothorax and venous occlusion between EPI and ENDO in children with atrioventricular block (AVB) or sinus node dysfunction (SND). Literature search was conducted in MEDLINE (via PubMed), Scopus by ELSEVIER, Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science, and OpenGrey databases until June 25, 2022. Random-effects meta-analyses were performed to assess the pacing method’s effect on lead failure, threshold rise, post-implantation infection and battery depletion and secondarily on all-cause mortality, hemothorax and venous occlusion. Several sensitivity analyses were also performed. Of 22 studies initially retrieved, 18 were deemed eligible for systematic review and 15 for meta-analysis. Of 1348 pediatric patients that underwent EPI or ENDO implantation, 542 (40.2%) had a diagnosis of congenital heart disease (CHD). EPI was significantly associated with higher possibility of PM-lead failure [pooled odds ratio (pOR) 3.00, 95% confidence interval (CI) 2.05–4.39; I2 = 0%]; while possibility for threshold rise, post-implantation infection and battery depletion did not differ between the PM types. Regarding the secondary outcome, the mortality rates between EPI and ENDO did not differ. In sensitivity analyses the results were consistent results between the two PM types. The findings suggest that EPI may be associated with increased PM-lead failure compared to ENDO while threshold rise, infection, battery depletion and mortality rates did not differ.