A new fast and accurate parallel algorithm is developed for solution of moving body problems, with specific reference to store separation problems. The algorithm starts with the development of separate meshes for the moving body (store) and the aircraft wing, which are then connected by using mesh blanking and mesh filling algorithms automatically. Following the partitioning of the connected meshes for parallel computing and obtaining a steady state flow solution, the separation starts by using a dynamically deforming mesh algorithm coupled with the six-degree of freedom rigid body dynamics equations for the store. The solutions continue until severe mesh distortions are reached after which automatic remeshing and partitioning are done on a new mesh obtained by blanking and filling operations to continue with the solutions. As the store reaches far enough distances from the aircraft, the algorithm switches to a relative coordinates eliminating any need for mesh deformations and remeshing. The developed algorithms and the results are discussed with a sample problem, including the parallel efficiency on distributed computers.