On the background of increasing demands on the accuracy and capability of autonomous navigation systems, a proper selection of adequate and capable microprocessors for spaceborne navigation applications becomes more and more important. In the framework of the planned PRISMA formation flying mission, a comparison of the runtime performance of three microprocessors is performed. The microprocessors, involved in the tests, are the ARM7TDMI, the PowerPC823, and the LEON2. Based on a realistic test case, the absolute and relative run-time performance of the processors is measured and compared. In addition to the considered test case, estimates of the expected computation time are derived for the anticipated navigation tasks in the framework of the PRISMA mission. This comprises absolute and relative orbit prediction and determination as well as guidance and control algorithms for autonomous formation control.