In this study, a flexibility-based finite element method considering geometric and material nonlinearities is developed for analyzing steel-concrete frame structures. The stability functions obtained from the exact buckling solution of the beam-column subjected to end moments are used to accurately capture the second-order effects. The proposed method uses the force interpolation functions, including a moment magnification due to the axial force and lateral displacement. Thus, only one element per a physical member can account for the interaction between the bending moment and the axial force in a rational way. The proposed method applies the Newton method based on the load control and uses the secant stiffness method, which is computationally both efficient and stable. According to the evaluation result of this study, the proposed method consistently well predicts the nonlinear inelastic behavior of steel-concrete composite frames and gives good efficiency.