With the advantage of inherent responsiveness that can change the spectroscopic signals from “off” to “on” state in responding to targets (e. g. biological analytes/microenvironmental factors), activatable fluorescent probes have attracted extensive attention and made significant progress in the field of bioimaging and biosensing. Due to the high depth of tissue penetration, minimal tissue damage and negligible background signal at longer wavelengths, the development of second near‐infrared window (NIR‐II) fluorescent materials provides a new opportunity to develop activable fluorescent probes. Here, we summarized properties, advantages and disadvantages of mainly NIR‐II fluorophores (such as rare earth‐doped nanoparticles, quantum dots, single‐walled carbon nanotubes, small molecule dyes, conjugated polymers and gold nanoclusters), then overviewed current role and development of activatable NIR‐II fluorescent probes (AFPs) for biomedical applications including biosensing, bioimaging and therapeutic. The potential challenges and perspectives of AFPs in deep‐tissue imaging and clinical application are also discussed.