This paper presents a method of finite element (FE) modeling and analysis of the seismic behavior of fully prefabricated steel frames with end-plate joints, flexible braces and composite slabs. The main idea and objectives of this paper is to develop a finite element model with high accuracy, good stabilization and acceptable computational costs for the simulation of the cyclic behavior of multi-story steel frames with bolted end-plate joints and concrete slabs. Because of the apparent tension-compression asymmetry of flexible braces, and the complex connection details between slabs and steel structures, as well as the huge number of contact interactions between interfaces, the cyclic behavior of this type of frame cannot be simulated accurately with commonly used line-element models, shell element models, or multi-scale models. A quasi-static test of a full-scale three-story fully prefabricated steel frame under cyclic horizontal loads by the present authors was simulated with the finite element model. Hollow section box columns, I-section beams, end-plates, inner diaphragms and stiffeners were modeled using shell elements; high strength bolts and concrete slab were modeled with solid elements; and flexible braces and rebar were modeled with truss elements. In order to develop a mesh skill to reduce computational costs while ensuring calculation accuracy, several FEM models were built and validated against previous experimental studies: static testing of bolted T-stub connections and bolted tension splices, static and cyclic testing of bolted end-plate steel joints, push-out tests of stud shear connectors, as well as static and cyclic testing of bolted end-plate composite joints. To simulate the “elastic-yield-hardening in tension, and buckling-without capacity in compression” behavior of the flexible braces, a simplified model in ABAQUS based on truss elements was developed and validated against previous tests. Results showed that the proposed FE modeling method could accurately simulate the static and cyclic performance of bolted T-stub connections, bolted tension splices, bolted end-plate steel joints, stud shear connectors, bolted end-plate composite joints and flexibly braced steel frames. Deformation capacity, cyclic behavior, horizontal loading performance, energy dissipation and stiffness degradation of steel frames with bolted end-plate joints, prefabricated slabs and flexible braces could be accurately simulated by this FEM model, providing a practical and accurate modeling method for similar structures. In addition, further research on the structural seismic performance simulation, parametric study and seismic design method could be carried out using the finite element model developed in this paper.