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The etiology of pediatric cancers is unique, stemming from developmental dysregulation rather than acquired mutations from carcinogenic exposure. These diseases demonstrate vastly different underlying genetic and epigenetic alterations and unique tissue microenvironments which are only now beginning to be explored. While many pediatric cancers have seen improved overall and event-free survival rates thanks to innovations in diagnosis and treatment, many have seen little to no improvement in patient outcomes. This highlights a critical need for additional research into the underlying genetic and epigenetic alterations in these pathologies. Non-coding RNAs (ncRNAs) are functional RNA molecules known to regulate gene expression at epigenetic, transcriptional, and translational levels and can serve as biomarkers of disease. Here, we examine current knowledge of the roles of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in the onset, progression, and therapeutic response of pediatric solid tumors. We discuss the current and future potential and pitfalls of these molecules as therapeutics and biomarkers and highlight critical knowledge gaps where future research might provide insight to improve current therapeutic strategies and improve clinical outcomes.