Monitoring of stem cells migrating or homing to the targets is essential for the success of stem cell-based therapies. For non-invasive magnetic resonance imaging (MRI) to serially track cell migration, recent efforts have focused on labeling cells with MR contrast agents, such as superparamagnetic iron oxide (SPIO) particles The currently-available MR cell labeling techniques include simple incubation and magnetoelectroporation. We attempted to develop an alternative instant cell labeling technique, using ultrasound to facilitate MR-labeling of cells, called magneto-sonoporation (MSP), which is based on the fact that ultrasound can increase cell membrane permeability to external molecules. This technical development demonstrated the potential of using magnetosonoporation to facilitate MR labeling of stem cells, which may become a safe and efficient MR labeling approach to instantly label large amounts of stem cells for preclinical and clinical applications.