Near infrared (NIR)-excitable and NIR-emitting probes have fuelled advances in biomedical applications owing to their power in enabling deep tissue imaging, offering high image contrast and reducing phototoxicity. There are essentially three NIR biological windows, i.e., 700–950 nm (NIR I), 1000–1350 nm (NIR II) and 1550–1870 nm (NIR III). Recently emerging optical probes that can be excited by an 800 nm laser and emit in the NIR II or III windows, denoted as NIR I-to-NIR II/III, are particularly attractive. That is because the longer wavelengths in the NIR II and NIR III windows offer deeper penetration and higher signal to noise ratio than those in the NIR I window. NIR imaging has indeed become a quickly evolving field and, simultaneously, stimulated the further development of new classes of NIR I-to-NIR II/III inorganic fluorescent probes, which include PbS, Ag₂S-based quantum dots (QDs) and rare earth (RE) doped NPs (RENPs) that possess quite diverse optical properties and follow different emission mechanisms. This review summarizes the recent progress on material merits, synthetic routes, the rational choice of excitation in the NIR I window, NIR II/III emission optimization, and surface modification of aforementioned fluorescent probes. We also introduce the latest notable accomplishments enabled by these probes in fluorescence imaging, lifetime-based multiplexed imaging and photothermal therapy (PTT), together with a critical discussion of forthcoming challenges and perspectives for clinic use.