The transition of wheel-rail contact point between the wheel tread and wheel flange in a flange bearing frog crossing (FBFC) is more complex than in a common crossing, which causes severe frictional rolling contact behavior and wheel-rail dynamic impact. This paper presents an analysis of the transient wheel-rail frictional rolling impact contact using an explicit finite element model of the dynamic interaction between the wheel and FBFC. This study adopts measured wheel geometry and an elastic-plastic material model for the simulations to provide an comprehensive understanding of the transient contact behavior of wheel-FBFC impacts. Each simulation calculates the evolution of the wheel-rail contact force, the distribution of micro-slips, and the stress during the wheel-FBFC impact. Then the contact damage mechanism is investigated and evaluated with the Zobory frictional wear model and “Layer” rolling contact fatigue model. The simulation results show that the irregular structure of the flange bearing frog crossing causes significant wheel-rail dynamic interaction, with the maximum wheel-rail force occurring in the bearing flangeway. The ratio of the tangential contact force to the normal contact force can be exacerbated by the geometric discontinuity of the crossings during impact. The main failure mechanism for different sections in the flange bearing frog crossing is different.