The therapeutic potential of stem cell therapy critically depends on precise epigenetic regulation mediated by PIWI/piRNA complexes. This review synthesizes current literature to analyze the structure, interaction mechanisms, and epigenetic functions of PIWI proteins and their associated piRNAs (24–32 nt non-coding RNAs), with emphasis on stem cell therapy and disease modeling applications. PIWI/piRNA complexes critically regulate transcriptional control, chromatin remodeling, and stem cell plasticity. These complexes maintain stemness while promoting differentiation, serving as key biomarkers and therapeutic targets in cancers and skeletal disorders. However, translational challenges regarding specificity, delivery stability, and safety profiles persist. Advancing PIWI/piRNA-based therapeutics requires innovative technologies and expanded clinical validation to develop safe, targeted stem cell treatments for diverse pathologies.