A nonlinear two-node superelement is proposed for the modeling of flexible complex-shaped links for use in multibody simulations. Assuming that the elastic deformations with respect to a corotational reference frame remain small, substructuring methods may be used to obtain reduced mass and stiffness matrices from a linear finite element model. These matrices are used in the derivation of potential and kinetic energy expressions of the nonlinear two-node superelement. By evaluating Lagrange’s equations, expressions for the internal and external forces acting on the superelement can be obtained. The inertia forces of the superelement are derived in terms of absolute nodal velocities and accelerations, which greatly simplifies the dynamic formulation. Three examples are included. The first two examples are used to validate the method by comparing the results with those obtained from nonlinear beam element solutions. We consider a benchmark simulation of the spin-up motion of a flexible beam with uniform cross-section and a similar simulation in which the beam is simultaneously excited in the out-of-plane direction. Results from both examples show good agreement with simulation results obtained using nonlinear finite beam elements. In a third example, the method is applied to an unbalanced rotating shaft, illustrating the potential of the proposed methodology for a more complex geometry.