Stem cells are rare and unique precursor cells that participate in the building and rebuilding of tissues and organs during embryogenesis, postnatal growth, and injury repair. Stem cells are distinctively endowed with the ability to both self-renew and differentiate, such that they can replenish the stem cell pool while continuing to produce the differentiated daughter cells that are essential for tissue function. Stem cell self-renewal/differentiation decisions must be carefully controlled during organogenesis, tissue homeostasis, and regeneration, as failure in stem cell maintenance or activation can lead to progressive tissue wasting, while unchecked self-renewal is a hallmark of many cancers. Here, we review evidence implicating the Notch signaling pathway, an evolutionarily conserved cell fate determinant with widespread roles in a variety of tissues and organisms, as a crucial regulator of stem cell behavior. As discussed below, this pathway plays varied and critical roles at multiple stages of organismal development, in lineage-specific differentiation of pluripotent embryonic stem cells, and in controlling stem cell numbers and activity in the context of age-related tissue degeneration, injury-induced tissue repair, and malignancy.