Hemodynamic forces, specifically fluid shear stress, play an important role in the focal nature of arterial plaque formation known as atherosclerosis. We hereby developed biocompatible and flexible intravascular microelectromechanical systems sensor to measure real-time shear stress in the aortas of New Zealand White (NZW) rabbits. Titanium (Ti) and platinum (Pt) were deposited on silicon wafers and patterned to form the sensing elements. The polymer, parylene C, provided insulation to the electrode leads and flexibility to the sensors. Based on heat transfer principle, the heat dissipation from the sensors to the blood flow altered the resistance of the sensing elements, from which shear stress was calibrated. The resistance of the sensing element was measured at approximately 1.0 kω, and the temperature coefficient of resistance was at approximately 0.16%/°C. The individual sensors were packaged to the catheter for intravascular deployment in the aortas of NZW rabbits (n=5). The sensor was capable of resolving spatial- and time-varying components of shear stress in the abdominal aorta. Computational fluid dynamic code based on non-Newtonian fluid properties showed comparable results within an acceptable range of experimental errors (±5) for the maximal and minimal values in shear stress during one cardiac cycle. Therefore, we demonstrated the capability of biocompatible sensors for real-time shear stress measurement in vivo with a potential to advance the understanding between the blood flow and vascular disease.