The cell cycle is a complex and strictly controlled process, consisting of different phases. Cell cycle regulation depends on phase-specific transcriptions of cell cycle genes. The alterations of cell cycle genes can predispose normal cells to have a cancerous phenotype. Indeed, several mechanisms underlying the deregulation of the cell cycle have been identified in different types of cancer. Cancer stem cells (CSCs), a fraction of tumor cells, are selectively capable of initiating tumor development. However, the deregulation of the cell cycle progression in CSCs still remains incompletely understood. This review describes epigenetic alterations and aberrant transcriptional regulation of cell cycle genes in CSCs as well as cell cycle patterns of CSCs.