Deep vein thrombosis, pulmonary embolism, and abdominal aortic aneurysms are blood-related diseases that represent a major public health problem. These diseases are characterized by the formation of a thrombus (i.e., blood clot) that either blocks a major artery or causes an aortic rupture. Identifying the mechanical properties of thrombi can help determine when these incidents will occur. In this investigation, a murine thrombus, formed from platelet-rich plasma, calcium, and thrombin, was nanoindented and the elastic modulus was determined via elastic contact theory. This information was used as input to an inverse finite element simulation, which synthesized optimal values for the elastic modulus and viscosity of the thrombus using a viscoelastic material model. A sensitivity analysis was also performed to determine which material parameters have the greatest affect on the simulation. Results from this investigation demonstrate the feasibility of the mechanical characterization of a murine thrombus using nanoindentation.