It is unclear whether there is a difference in outcomes with treosulfan or busulfan-based conditioning in pediatric patients undergoing hematopoietic stem cell transplantation (HSCT). We reviewed the evidence on this topic through a systematic review and meta-analysis, the comparison between treosulfan and busulfan-based conditioning in pediatric patients undergoing HSCT for instance. Six studies were included. Meta-analysis showed that there was no difference in the incidence of acute graft versus host disease (odds ratio [OR]: 0.96; 95% CI: 0.57, 1.61), grade II to IV acute graft versus host disease (OR: 1.19; 95% CI: 0.83, 1.72), chronic GVHD (OR: 1.18; 95% CI: 0.70, 2.00), and veno-occlusive disease (OR: 0.92; 95% CI: 0.22, 3.85) between treosulfan and busulfan groups. Pooled analysis indicated marginally better survival with treosulfan-based conditioning (OR: 1.57; 95% CI: 1.00, 2.44), however, these results were unstable on sensitivity analysis. A meta-analysis found no difference in transplant-related mortality (OR: 0.70; 95% CI: 0.34, 1.42) between the two groups. Retrospective data from a heterogenous population indicates that there is no difference in the rate of GVHD after treosulfan versus busulfan-based conditioning for pediatric HSCT. A marginal improvement in survival was noted with treosulfan but the results remained unstable. Future randomized controlled trials are needed to provide better evidence.