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Abstract Photoacoustic tomography (PAT) with genetically encoded near‐infrared probes enables visualization of specific cell populations in vivo at high resolution deeply in biological tissues. However, because of a lack of proper probes, PAT of cellular dynamics remains unexplored. Here, the authors report a near‐infrared Forster resonance energy transfer (FRET) biosensor based on a miRFP670‐iRFP720 pair of the near‐infrared fluorescent proteins, which enables dynamic functional imaging of active biological processes in deep tissues. By photoacoustically detecting the changes in the optical absorption of the miRFP670 FRET‐donor, they monitored cell apoptosis in deep tissue at high spatiotemporal resolution using PAT. Specifically, they detected apoptosis in single cells at a resolution of ≈3 µm in a mouse ear tumor, and in deep brain tumors (>3 mm beneath the scalp) of living mice at a spatial resolution of ≈150 µm with a 20 Hz frame rate. These results open the way for high‐resolution photoacoustic imaging of dynamic biological processes in deep tissues using NIR biosensors and PAT.