In recent years, several large earthquakes have caused the collapse of container cranes, which have resulted in halting of freighting, and significantly affected the economy. Some reports are concerned the uplift and derailment events of crane legs, and the collapse of the crane itself. In this study, the effects of different boundary conditions used in the numerical method are investigated for a container crane under seismic excitation. Three different boundary conditions are considered in terms of the connection of the crane’s legs (wheels) and the ground (rails), namely pin support (PIN), gap element (GAP), and Friction contact (FC) elements, by using the SAP2000 program for a typical container crane. Then, time history dynamic analyses are conducted using nine recorded ground motions. Dynamic behaviors of the container crane are studied in terms of the total base shear, portal drift, and relative displacement of legs, by investigating the three types of base boundary conditions. The results of the study show that when the intensity of earthquakes is large enough to create uplift and derailment events, the selection of the boundary condition model considerably affects the dynamic responses of the container crane. In addition, when uplift and derailment of the crane occur, the FC support condition is the most compatible with the real behavior of the crane. On the other hand, under low seismic excitation, there is no significant difference of the crane behavior according to the choice of boundary condition model.