Carbon-based nanomaterials such as graphene sheets and carbon nanotubes possess unique mechanical, electrical, and optical properties that present new opportunities for tissue engineering, a key field for the development of biological alternatives that repair or replace whole or a portion of tissue. Carbon nanomaterials can also provide a similar microenvironment as like a biological extracellular matrix in terms of chemical composition and physical structure, making them a potential candidate for the development of artificial scaffolds. In this review, we summarize recent research advances in the effects of carbon nanomaterial-based substrates on cellular behaviors, including cell adhesion, proliferation, and differentiation into osteo- or neural- lineages. The development of 3D scaffolds based on carbon nanomaterials (or their composites with polymers and inorganic components) is introduced, and the potential of these constructs in tissue engineering, including toxicity issues, is discussed. Future perspectives and emerging challenges are also highlighted.