Novel strategies utilizing magnetic nanoparticles (MNPs) and magnetic fields are being developed to enhance bone tissue engineering efficacy. This article first reviewed cutting-edge research on the osteogenic enhancements via magnetic fields and MNPs. Then the current developments in magnetic strategies to improve the cells, scaffolds and growth factor deliveries were described. The magnetic-cell strategies included cell labeling, targeting, patterning, and gene modifications. MNPs were incorporated to fabricate magnetic composite scaffolds, as well as to construct delivery systems for growth factors, drugs and gene transfections. The novel methods using magnetic nanoparticles and scaffolds with magnetic fields and stem cells increased the osteogenic differentiation, angiogenesis and bone regeneration by 2–3 folds over those of the controls. The mechanisms of magnetic nanoparticles and scaffolds with magnetic fields and stem cells to enhance bone regeneration were identified as involving the activation of signaling pathways including MAPK, integrin, BMP and NF-κB. Potential clinical applications of magnetic nanoparticles and scaffolds with magnetic fields and stem cells include dental, craniofacial and orthopedic treatments with substantially increased bone repair and regeneration efficacy.