To determine whether magnetic resonance imaging (MRI) can enable magnetically labeled mesenchymal stem cell (MSC) tracking and simultaneous in vivo functional data acquisition in rat models of myocardial infarction. Superparamagnetic iron oxide-laden human MSCs were injected into rat myocardium infarcted by cryoinjury 3 weeks after myocardial infarction. The control group received cell-free media injection. Before injection and for 3 months after, in vivo serial MRI was performed. Electrocardiography-gated gradient echo sequence MRI and cine MRI were performed for in vivo cell tracking and assessing cardiac function using left ventricular ejection fraction (LVEF), respectively. MRI revealed a persistent signal-void representing iron-laden MSCs until ten post-injection weeks. Serial follow-up MRI revealed that LVEF was significantly higher in the MSC injection group than in the control group. We conclude that MRI enables in vivo tracking of injected cells and evaluation of the long-term therapeutic potential of MSCs for myocardial infarction.