A new fully automated store-trajectory simulation code has been developed. The method couples a highly robust computational fluid dynamics method and a cut-paste algorithm for Chimera domain decomposition to enhance the efficiency of store-trajectory simulation. The time-step size limitation caused by grid movement is relaxed with the interpolation of solutions in the previous time step. A treatment for orphan cells is also devised to improve the robustness of the method. The computational results show that the current method is capable of simulating store separation without user interruption and that a time-step size of 0.005 s, which is more than three times larger than ever reported, can be used for the Eglin Wing/Pylon/Store separation problem.