In this paper, a new modified finite element method that can be used in the analysis of transverse and lateral vibrations of the thin beams under a point mass moving with a variable acceleration and constant jerk is presented. Jerk is the change in acceleration over time. In this method, the classical finite element of the beam is modified by the inclusion of the inertial effects of the moving mass. This modification is made using the relations between nodal forces and nodal deflections and shape functions of six DOF beam element. The mass, stiffness, and damping matrices of the modified finite element are determined by forces caused by the corresponding transverse and lateral accelerations and jerks, and transverse Coriolis and centripetal accelerations and jerks, respectively. This method was first applied on a simply supported beam plate to provide a comparison with the previous studies in literature, and it was proved that the results were within acceptable limits. Secondly, it was applied on a CNC type box-framed beam to analyse the dynamic response of the beam in terms of variable acceleration and jerk as well as constant velocity and mass ratios.