Apoptosis plays crucial roles during development and in disease conditions. While there are some methods to detect apoptosis in vitro, most of them are end-point assays that cannot be used to detect apoptosis in the physiological context of live animals. In this study, transgenic sensor zebrafish were generated that specifically produce a fluorescence resonance energy transfer (FRET)-based biosensor in the zebrafish skin. Under normal conditions, the skin cells of the sensor zebrafish emit green fluorescence; when caspase-3 is activated during apoptosis, the skin cells of the sensor zebrafish switch to emitting blue fluorescence. Through time-lapse FRET imaging with the sensor zebrafish, we observed that caspase-3 can be activated within 5 min and apoptosis can be completed in around 30 min in live zebrafish, no matter the apoptosis occurs several hours after UV irradiation or during the normal development. Using the sensor zebrafish, we found that apoptosis can occur in different parts of the zebrafish skin including the skin covering the trunk, eye, yolk sac, and head during development. Interestingly, we observed that the yolk sac diameter of the zebrafish reduced from 723.8 ± 25.1 μm at 24 h postfertilization (hpf) to 346.1 ± 24.6 μm at 120 hpf. To accommodate this dramatic reduction of the yolk sac size, we found that some excess skin cells on the surface of the yolk sac were removed by apoptosis during this process. The sensor zebrafish provide a powerful and convenient tool for the noninvasive and real-time detection of apoptosis at the single-cell resolution in live zebrafish.