Stroke is a refractory cerebral blood circulation disorder. Endothelial progenitor cells (EPCs) participate in the repair and regeneration of vascular injury through the combination of cell replacement and bystander effects. Here, we evaluated the biological function of EPCs in treating a mouse model of cerebral ischaemic stroke, using dual-mode bioluminescence and magnetic resonance imaging to trace EPCs in vivo. We constructed a viral vector with a luciferase-enhanced green fluorescent protein (Luc-eGFP) reporter gene for bioluminescence imaging (BLI) detection, and simultaneously synthesized the magnetic resonance imaging (MRI) contrast agent, nano-sized superparamagnetic iron oxide (USPIO), to co-label human umbilical cord blood-derived EPCs (hEPCs). The labelled hEPCs were transplanted into mice with stroke, and the biological behaviours of the cells in-vivo were studied using BLI and MRI, and methods of molecular biology and histology. Comparing the two cell transplantation routes by BLI confirmed that many cells transplanted via the left ventricular route homed to ischaemic brain tissue. The dual-modality-imaging showed the prognosis of in-vivo tracking cells after transplantation in ischaemic tissues at different time points. Histological staining and neurological function scores confirmed that EPC transplantation can improve the symptoms of nerve deficit in the mouse stroke model. Histological staining revealed that cell transplantation can lead to recovery of neurological function after stroke, via various processes. These include reduced blood brain barrier permeability, recovery of white matter and of myelin, and the enhancement of neuroneogenesis. Dual-modality imaging revealed EPCs as potential candidates for the treatment of ischaemic stroke. Copyright © 2019. Published by Elsevier Inc.