Macroautophagy is widely accepted as a cytoprotective mechanism against various environmental stresses. While inhibition of autophagy is generally considered to increase the susceptibility of cancer cells to therapeutic agents, whether it also plays a similar role in tumor stem cells is unclear and still controversial. With increased attention and efforts focused on the cytoprotective feature of autophagy in cancer, it is also essential to understand its role in the biology of cancer stem cells, including self-renewal, differentiation, and tumorigenicity. Although there are very few studies that evaluate autophagy in cancer stem/progenitor cells, understanding the mechanisms governing autophagic responses in various cancer stem cells could provide support for the future development of clinical therapeutics. The present review summarizes current studies that assess the role of autophagy in various types of cancer stem cells and those that evaluate the application of inhibitors of key components within the autophagy pathway in cancer stem/progenitor cells.