This paper presents an investigation of the dynamic behavior of bi-directionally functionally graded (BDFG) micro/nanobeams excited by a moving harmonic load. The formulation is established in the context of the surface elasticity theory and the modified couple stress theory to incorporate the effects of surface energy and microstructure, respectively. Based on the generalized elasticity theory and the parabolic shear deformation beam theory, the nonclassical governing equations of the problem are obtained using Lagrange’s equation accounting for the physical neutral plane concept. The material properties of the beam smoothly change along both the axial and thickness directions according to power-law distribution, accounting for the gradation of the material length scale parameter and the surface parameters, i.e., residual surface stress, two surface elastic constants, and surface mass density. Using trigonometric Ritz method (TRM), the trial functions denoting transverse, axial deflections, and rotation of the cross sections of the beam are expressed in sinusoidal form. Then, with the aid of Lagrange’s equation, the system of equations of motion are derived. Finally, Newmark method is employed to find the dynamic responses of BDFG subjected to a moving harmonic load. To validate the present formulation and solution method, some comparisons of the obtained fundamental frequency and dynamic response with those available in the literature are performed. A parametric study is performed to extensively explore the impact of the key parameters such as the gradient indices in both directions, moving speed, and excitation frequency of the acting load on the dynamic response of BDFG nanobeams. The obtained results can serve as a guideline for assessing the multi-functional and optimal design of micro/nanobeams acted upon by a moving load.