Thrombin, a kind of serine protease, is a significant regulator of thrombosis in vivo. Herein, we proposed a label-free and sensitive fluorescent assay for probing thrombin activity based on an enhanced green fluorescence protein (EGFP) probe and gold nanoparticles (AuNPs). The EGFP probe containing a hexahistidine sequence (His-tag) and a thrombin recognition site at the N-terminal was designed. His-tag enables the probe be adsorbed on the surface of AuNPs through high affinity of His-Au bond, and in consequence fluorescence resonance energy transfer (FRET) would happen, where EGFP is the fluorescence donor and AuNPs as the acceptor. Because of the high extinction coefficient of AuNPs, the fluorescence of EGFP will be quenched. When there is thrombin, it cleaves the recognition site, and results in the leaving of His-tag from EGFP. EGFP without His-tag cannot be efficiently adhered on AuNPs, and its fluorescence is protected. Thus, the corresponding fluorescence signal can respond to the activity of thrombin. Using this turn-on fluorescence assay, we obtained a high sensitive and special detection for thrombin activity (limit of detection = 0.0025 U/mL) with the linear range from 0.01 U/mL to 0.25 U/mL under optimized conditions. The assay can also be used to measure the inhibition of thrombin activity (where hirudin was used as an example) with an IC50 value of 1.38 nM, and was successfully performed in real sample. Furthermore, the proposed assay has the potential to be a fluorescence-colorimetry dual detection method.