In recent years, with increasing demands for in vivo fluorescence imaging and photodynamic therapy, light in the second near‐infrared window (NIR‐II; 1000–1700 nm) has attracted tremendous interest because it offers numerous merits, including deep penetration, minimal phototoxicity, diminished tissue autofluorescence, and reduced tissue absorption and scattering. Among the diverse types of nanoparticles, organic nanoprobes with aggregation‐induced emission (AIE) characteristics have emerged as a better option owing to their ultra‐brightness, excellent photostability, low cytotoxicity, and tailorable optical properties. Recent efforts in the AIE realm have revealed advancements in molecular design for long wavelength absorption and multiphoton excitation, which efficiently modulate the working optical region to the NIR‐II region. In this review, the current status of AIE nanoprobes in the NIR‐II window is summarized. Starting with molecular design strategies, recent efforts in fluorescence imaging and photodynamic therapy are then discussed. Finally, perspectives and challenges in this newly emerging field are given. This review hopes to encourage more innovative ideas in material design and biomedical applications for promoting AIE nanoprobes for future clinical translation.