Thrombosis is an adverse physiological event wherein the resulting thrombus and thrombus‐induced diseases collectively result in high morbidity and mortality rates. Currently, nano‐medicines that incorporate fluorophores emitting in the near‐infrared‐I (NIR‐I, 700–900 nm) spectral region have been adopted to afford thrombosis theranostics. However, several unsolved problems such as limited penetration depth and image quality severely impede further applications of such nano‐medicine systems. Fortunately, the ability to incorporate fluorophores emitting in the NIR‐II (1000–1700 nm) window into nano‐medicine systems can unambiguously identify biological processes with high signal‐to‐noise, deep tissue penetration depth, and high image resolution. Considering the inherently favorable properties of NIR‐II fluorophores, it is believed that they have enormous potential to quickly become incorporated into nano‐medicine systems for thrombosis theranostics. In this review, i) the development of NIR fluorescence as an imaging modality and fluorescent agents is discussed; ii) the recent development of NIR‐I fluorophore‐based nano‐medicine systems for thrombosis theranostics is comprehensively summarized; iii) the state‐of‐the‐art NIR‐II fluorophores that are designed for the specific purpose of affording thrombotic diagnosis is highlighted; iv) possible forward avenues for the use of NIR‐II fluorophores toward thrombosis diagnosis and therapy are speculated; and v) the potential for their clinical translation is discussed.