Abstract This paper presents a direct time-domain three dimensional (3D) numerical procedure to simulate the transient response of very large floating structures (VLFS) subjected to unsteady external loads as well as moving mass. The proposed procedure employs the Boundary Element and Finite Element methods (FEM-BEM). The floating structure and the surrounding fluid are discretized by 4-node isoparametric finite elements (FE) and by 4-node constant boundary elements (BE), respectively. Structural analysis is based on Mindlin's plate theory. The equation of motion is constructed taking into account the effect of inertia loading due to the moving mass. In order to obtain the hydrodynamic forces (added mass and radiation damping), the coupled natural frequencies are first obtained by an iterative method, since hydrodynamic forces become frequency-dependent. Then the Newark integration method is employed to solve the equation of motion for structural system. In order to prove the validity of the present method, a FORTRAN program is developed and numerical examples are carried out to compare its results with those of published experimental results of a scale model of VLFS under a weight drop and airplane landing and takeoff in still water condition. The comparisons show very good agreement.