Motion control systems are gaining importance as more and more sophisticated developments arise in technology. Technological improvements enhance incorporation of different research areas into the same framework while trying to make systems function in unstructured environments renders the design of control systems increasingly complex. Since motion systems are complex, they have complex forward or inverse kinematics, or interactions with other systems. In this study, motion of the systems is decomposed into the tasks, so called “functions”. Independent controllers are designed for these functions in the function space. It is proven that motion systems will be controlled in the original space if function based control outputs are superposed. Applicability of this method is demonstrated on bilateral systems and parallel mechanisms. Bilateral systems application proved that function based control can be used in controlling systems with interactions while establishing desired functional relation between them. Moreover, investigation of a pantograph and a three-legged manipulator, which come from the parallel mechanisms family and have nonlinear and coupled system dynamics, showed that creating an appropriate reference configuration to realize the task of motion control helps decouple system dynamics. Satisfactory simulation results show that functional control can be implemented and its characteristics promise successful future designs for motion control systems