Ischemia-reperfusion injury (IRI) in different organs is a common pathophysiological basis in a variety of clinical critical diseases, such as myocardial infarction, cerebral stroke, and organ transplantation. The early diagnosis and real-time monitoring of IRI is unequivocally of great significance in revealing the underlying pathogenesis, evaluating tissue activity, and improving prognosis. Near-infrared (NIR) fluorescence imaging technology has displayed great potential in investigating IRI via the manner of in vivo real-time visualization. As the cornerstone involved in such a technology, fluorescent probes play a crucial role therein, and their design strategy and performance dominantly determine the imaging specificity, sensitivity, and evaluation ability. This minireview aims to outline recent advances in research dedicated to the diagnostic applications of NIR fluorescent probes via IRI imaging, with a focus on the pathophysiological mechanism of IRI and the key biomarkers that generally act as the basis of probe design. Additionally, we classify and summarize the imaging applications of fluorescent probes according to their involvement in various IRI models of important organs, including heart, brain, lung, liver, kidney, and limbs, and give an insight into the key to design rationale and imaging performance of the probes. Finally, we present a viewpoint towards the key challenges in NIR fluorescence imaging for mapping IRI and the future research regarding developing more versatile and more efficient NIR fluorescent probes for IRI clinical imaging applications.