The hedgehog (Hh) signaling pathway is an evolutionarily conserved pathway that regulates embryonic development in vertebrates. However, strong evidence suggests the role of its dysregulation in human diseases, especially cancers. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), belong to a group of human transcriptomes that do not translate into proteins. However, they can highly influence protein expression. This review will provide a comprehensive link between ncRNAs and Hh signaling pathways in different human diseases and development, providing insights into disease and cancer progression as well as emphasizing their therapeutic, prognostic, and diagnostic significance.