Thioredoxin reductase (TrxR) enzymes are critical in regulating redox homeostasis in cells. We report the first two-photon fluorescent probe of mammalian TrxR (TP-TRFS). TP-TRFS retains high specificity in recognizing TrxR. More importantly, the two-photon absorbing character of TP-TRFS enables it to be used in vivo. With the aid of TP-TRFS, a remarkable decline of the TrxR function was observed in the brain of a mouse model of stroke for the first time, providing a mechanistic link of TrxR dysfunction with stroke.