A new three-dimensional moving Timoshenko beam element is developed for dynamic analysis of a moving load problem with a very long beam structure. The beam has small deformations and rotations, and bending, shear, and torsional deformations of the beam are considered. Since the dynamic responses of the beam are concentrated on a small region around the moving load and most of the long beam is at rest, owing to the damping effect, the beam is truncated with a finite length. A control volume that is attached to the moving load is introduced, which encloses the truncated beam, and a reference coordinate system is established on the left end of the truncated beam. The arbitrary Lagrangian–Euler method is used to describe the relationship of the position of a particle on the beam between the reference coordinate system and the global coordinate system. The truncated beam is spatially discretized using the current beam elements. Governing equations of a moving element are derived using Lagrange’s equations. While the whole beam needs to be discretized in the finite element method or modeled in the modal superposition method (MSM), only the truncated beam is discretized in the current formulation, which greatly reduces degrees-of-freedom and increases the efficiency. Furthermore, the efficiency of the present beam element is independent of the moving load speed, and the critical or supercritical speed range of the moving load can be analyzed through the present method. After the validation of the current formulation, a dynamic analysis of three-dimensional train–track interaction with a non-ballasted track is conducted. Results are in excellent agreement with those from the commercial software simpack where the MSM is used, and the calculation time of the current formulation is one-third of that of simpack. The current beam element is accurate and more efficient than the MSM for moving load problems of long three-dimensional beams. The derivation of the current beam element is straightforward, and the beam element can be easily extended for various other moving load problems.