Stem cells are one of the key components in tissue engineering (TE) for tissue repair and regeneration. However, further studies are necessary in order to provide a suitable microenvironment for stem cells to differentiate and thereby regenerate tissues. Carbon-based nanomaterials (i.e., carbon nanotubes (CNTs) and graphene) have recently attracted much significant attention as tools for investigating and controlling stem cell biology and fate due to their remarkable characteristics, including unique mechanical properties, tunable surface chemistry, and high electrical conductivity. In this review paper, we describe applications of CNTs and graphene in stem cell differentiation and consequently tissue formation in both in vitro and in vivo conditions. Cytotoxicity of CNTs and graphene is also addressed. Finally, we discuss potential challenges and future directions for applications of CNTs and graphene in the stem cell culture and differentiation.