Nanotechnology in stem cell medicine is an interdisciplinary field which has gained a lot of interest recently. This domain addresses key challenges associated with stem cell medicine such as cell isolation, targeted delivery, and tracking. Nanotechnology-based approaches, including magnetic cell sorting, fluorescent tagging, and drug or biomolecule conjugation for delivery, have enhanced precision in stem cell isolation and guided cell migration, increasing the therapeutic potential. Recent studies have focused on using nanomaterials and scaffolds to drive stem cell differentiation by activating specific molecular pathways, achieved through embedding biomolecules within the scaffold or through the scaffold's material composition and structure alone. These innovations hold promise in therapeutic applications across various diseases, including cancer stem cell targeting, neurodegenerative disorders, pre-eclampsia, cardiovascular conditions, and organoid development. This review examines recent advancements in the field, explores potential applications like biosensors and nanochips, and highlights the challenges and research gaps.