It is known that the intensity of surface-enhanced Raman scattering (SERS) of monomeric gold nanoparticles (GNPs) is insufficient for ultrasensitive analysis. The authors describe dimeric GNPs for use in a competitive SERS and aptamer based assay for thrombin. The reagent 1,2-bis(4-pyridyl) ethylene serves as both the coupling agent and the Raman reporter on the GNP dimers. In the presence of thrombin, the hybridization of two aptamers, one attached to the GNP dimers, the other to magnetic nanoparticles, is competitively prevented. This method takes advantage of the unique "hot spots" of the GNP dimers to amplify the Raman signal. This results in an ultra-sensitive thrombin assay when compared to assays using GNP monomers. The limit of detection is as low as 1 fM of thrombin. The Raman intensity, best measured at 1612 cm, increases linearly in the 1 fM to 10 nM thrombin concentration range. The method was applied to the determinaiton of thrombin in spiked simulated body fluid and human serum. Graphical abstract This method takes advantage of the unique "hot spots" of the gold nanoparticle dimers to amplify the Raman signal. The dimers are linked to the magnetic nanoparticles via an aptamer. The use of both competitive displacement and magnetic separation greatly improves the sensitivity of the thrombin assay.