Stem cell-based therapies hold great promise as alternative therapeutic strategies for various chronic diseases, including ischemic cardiomyopathy. Tracking the engraftment of transplanted stem cells is critical to the assessment of donor cell survival in the host environment. Fluorescent proteins, such as green fluorescent protein (GFP), have been widely used to track the fate of donor cells; however, GFP labeling has limitations with regard to noninvasively measuring cell engraftment in vivo. Our research indicates that near-infrared fluorescent protein (iRFP) labeling offers advantages for noninvasive in vivo imaging and histological assessment. Here, we present a protocol for using the lentiviral vector-mediated iRFP vector system to label and track donor stem cells in ischemic mouse hearts.