We present the enhanced magnetotransport and thermal properties of FeMn exchange-biased magnetic tunnel junctions (MTJs) by rapid thermal anneal (RTA). The tunneling magnetoresistance (TMR) in an as-grown MTJ is found to be 27%, while the TMR in MTJs annealed by RTA ( < 2 min.) increases with annealing temperature up to 300 ^oC, reaching 46%. TEM images reveal a significant structural change at the interface of Al₂O₃ layer for the MTJ annealed by RTA, which is attributable to oxygen redistribution and homogenization in the insulating layer during RTA, leading to the improvement of TMR. We also found that remarkable changes in effective barrier thickness and height occur within a few ten seconds during RTA, indicating that the structural transformation in the oxide barrier takes place abruptly at the initial step of the anneal. More importantly, we found that RTA provides structural robustness for MTJs, resulting in a heat-resistant junction structure to a subsequent thermal treatment. It is believed to be due to an additional RTA effect to reduce structural defects in the CoFe pinned layer, preventing the interdiffusion of Mn at the interface of CoFe and FeMn or the diffusion of Mn to the oxide barrier. We discuss the detailed mechanism for the enhanced thermal stability by RTA with the results of soft X-ray fluorescence spectroscopy and Auger electron spectroscopy.