The ubiquitin (Ub) system, a ubiquitous presence across eukaryotes, plays a crucial role in in the precise orchestration of diverse cellular protein processes. From steering cellular signaling pathways and orchestrating cell cycle progression to guiding receptor trafficking and modulating immune responses. The dysregulation of Ub-mediated signaling pathways in prevalent cancers ushers in a spectrum of clinical outcomes ranging from tumorigenesis and metastasis to recurrence and drug resistance. Ubiquitination, a linchpin process mediated by Ub, assumes a central mantle in molding cellular signaling dynamics. It navigates transitions in biological cues and ultimately shapes the destiny of proteins. Recent years have witnessed an upsurge in the momentum surrounding the development of protein-based therapeutics aimed at targeting the Ub system under the sway of cancer stem cells (CSCs). The article provides a comprehensive overview of the ongoing in-depth discussions regarding the regulation of the Ub system and its impact on the development of CSCs. Amidst the tapestry of insights, the article delves into the expansive roles of E3 Ub ligases, deubiquitinases (DUBs), transcription factors entwined with CSCs. Furthermore, the spotlight turns to the interplay with pivotal signaling pathways the Notch, Hedgehog (Hh), Wnt/β-catenin, and Hippo-YAP signaling pathways all play crucial roles in regulation of CSCs following by the specific modulation of Ub-proteasome.