Yes-associated protein 1 (YAP1) is a downstream effector of the Hippo signaling pathway, and it is involved in tumorigenesis, tissue repair, growth, and development. In this review, the biological roles and the mechanisms of YAP1 in mediating stem cell fate decisions are discussed, including cell proliferation, differentiation, and apoptosis. In general, YAP1 promotes the proliferation and differentiation of stem cells, including embryonic stem cells and adult stem cells. It inhibits apoptosis by binding to the transcription factors, e.g., transcriptional enhanced associate domain (TEAD), Smad, runt-related transcription factor 1/2, p73, p63, and Erb84, to maintain tissue homeostasis. The translocalization of YAP1 in cellular nuclei and the phosphorylation in the cytoplasm work as important and unusual events for the activation of YAP1. Moreover, YAP1 serves as the crosstalk for the Hippo pathway and other signaling pathways, including the Wnt and Notch pathways. It is highlighted in this review that YAP1 is an essential regulator for stem cells that have significant applications in regenerative medicine and reproductive medicine.