Background HLA epitope‐based matching offers the potential to improve immunological risk prediction and management in children receiving renal allografts; however, studies demonstrating the association between systems for defining epitope mismatches and clinical end‐points are lacking in this population. Methods We conducted a pragmatic, retrospective, registry‐based study of pediatric recipients of primary renal allografts in Victoria, Australia between 1990 and 2014 to determine the association between HLA EpMM and clinical outcomes including graft failure, re‐transplantation and dnDSA formation. Results A total of 196 patients were included in the analysis with a median age of 11 years. Median follow‐up period was 15 years during which time 108 (55%) primary grafts failed and 72 patients were re‐transplanted. HLA class I but not class II EpMM was a significant predictor of graft failure on univariate analysis but not in adjusted models. EpMM was associated with reduced likelihood of re‐transplantation in univariate but not adjusted analysis. Within the limitations of the study, class‐specific EpMM was a strong predictor of dnDSA formation. Associations were stronger when considering only the subset of antibody‐verified EpMM. Conclusion Associations between HLA EpMM and clinical outcomes in pediatric renal allograft recipients seen on univariate analysis were attenuated following adjustment for confounders. These findings are inconclusive but suggest that HLA EpMM may provide one tool for assessing long‐term risk in this population while highlighting the need for further clinical studies.