The growing evidence suggests that the disturbance of redox homeostasis in the brain tissue contributes to the process of tissue damage following ischemic stroke (IS). Tracking redox process in situ is critical for diagnosis, treatment and drug design of IS. Monitoring of substances in the reduction system is more suitable than detection of molecules of oxidation system, such as reactive oxygen species (ROS), due to their difficult capture of fleeting existence. Glutathione (GSH), a dominated component of reduction system, has higher concentration than other reduced substances and is the major cellular antioxidant for maintaining the redox balance but dramatically decreases during cerebral ischemia. Efficient tools can realize the real-time tracing of endogenous GSH at ultra low concentration during ischemic damage are significant and indispensable for dynamic monitoring the process of IS. Till now, only a few fluorescent probes have been reported for imaging GSH. The direct visualization of reductive substances in the cerebral vasculature of live mice is still a significant challenge. More importantly, due to the presence of the blood–brain barrier (BBB), monitoring GSH at ultralow concentration in brain tissue seems more difficult, which tremendously restricts the development of new strategies for targeting, detecting, and imaging GSH in vivo. In present study, we successfully synthesized a series of BODIPY-based fluorescent probes, WD-1-SH, WD-2-SH, and WD-3-SH, and detected many properties, including the capacity to penetrate the BBB, sensitivity to GSH and tissue penetration depth of excitation, and emission wavelengths. In vitro experiments revealed that among the probes, WD-1-SH exhibited the highest sensitivity to reducing substances; however, WD-2-SH exhibited higher sensitivity in vivo. These desired photophysical and pharmacokinetic properties endow our fluorescent probes with the capability to monitor brain tissue low concentration GSH after injury with excellent temporal and spatial resolution. Due to these favourable properties, our fluorescent probes hold great promise for visualizing endogenous reducing substances in a variety of pathophysiological processs in vitro and in vivo, such as during stroke induced ferroptosis.