Stem-cell based therapy strategies are promising approaches for the treatment of bone defects. However, extensive cell expansion steps, the low rate of cell survival and uncontrolled differentiation of stem cells transplanted into the body currently remain key challenges in advancing stem cell therapeutics. An alternative strategy is to use specifically designed bone scaffolds to recruit endogenous stem cells upon implantation and to stimulate new bone formation and remodeling. Stem cell recruitment based on scaffold features for bone tissue engineering relies on the development of scaffolds that can effectively mobilize and recruit endogenous stem cells to the implantation site. This article addresses the recent advances in the recruitment of endogenous stem cells in applications of bone scaffolds, particularly focusing on chemical modification and physical characteristic modification of the scaffold for endogenous stem cell homing and recruitment. Finally, the continuing challenges and future directions of scaffold-based stem cell recruitment are discussed.