Recent advances in the study of dynamics of multibody systems indicate the need for decoupling of the equations of motion. In this paper, our efforts are focused on this issue, and we have tried to expand the existing methods for multi-rigid body systems to include systems with some kind of flexibility. In this regard, the equations of motion for a planar two-degree-of-freedom robot with flexible joints is carried out using Lagrange’s equations and Kane’s equations with congruency transformations. The method of decoupling the equations of motion using Kane’s equations with congruency transformations is presented. Finally, the results obtained from both methods are compared.