Turnouts are among the weakest links of railway lines, but the derailment risk of vehicles passing the through route of a turnout is seldom considered. The potential factors affecting derailment are screened according to field investigations of a train derailment case at the through route of a turnout. A detailed wagon-turnout interaction model considering the non-uniform cross-sections of turnout rails and the interaction between adjacent wagons is developed and validated. Through numerical simulation, the dynamic performance of an empty wagon passing the through route of turnout at a low speed is studied. When the wagon passes the turnout under the continuous lateral force condition, the wheels climb onto the rail head at the switch area in the facing direction, while the derailment occurs at the frog area in the trailing direction. Moreover, the possibility of derailment of the empty wagon increases with increasing coupler force and wheel-rail friction coefficient, and with decreasing speed. To improve the safety of empty wagons in the turnout area, rail lubrication should be implemented to reduce the wheel-rail friction coefficient, and large braking forces should be avoided. Furthermore, the wheel surface condition after re-profiling requires continuous attention.