In this work, the effects of rapid thermal annealing on the electrical and structural properties of Mo/SiC Schottky contacts which fabricated by FTS system were investigated. As-fabricated Mo/SiC Schottky contacts were thermally treated in Ar atmosphere at the temperature of 500-700 degrees C, for 120s. By the rapid thermal annealing process, the SBHs of diodes were decreased while other parameters including series resistance and ideality factor were not changed significantly. However significant degradation in reverse blocking performance was occurred with the annealing temperature of 700 degrees C. This was in tendency of proportional to the thickness of interfacial layers between Mo and SiC. Optimal annealing condition for Mo/SiC Schottky contacts was found to be at 600 degrees C for 120 sec.