This study aims to reduce the earthquake-induced vibrations of the container crane structures using an active vibration control. Vibration control using intelligent controllers such as fuzzy logic has attracted the attention of structural control engineers during the last decade. Fuzzy logic can handle uncertainties and heuristic knowledge and even nonlinearities effectively and easily. The improved seismic control performance can be performed by converting a simply designed static gain into a real time variable dynamic gain through a self-tuning mechanism. Because of the several advantages, the self-tuning fuzzy logic control algorithm is used in this study. Furthermore, with the aim of the increasing the performance of the designed controller, derivative and integral controller which are independent from the fuzzy logic controller are added to the architectural structure of the controller. This structure is called as self-tuning fuzzy logic PID controller (STFLPIDC). In this study, a six-degrees-of-freedom nonlinear mathematical model of the container crane structure is defined. Then, the controller is developed. Performance of designed controller is evaluated by numerical simulations. In the simulations, the ground motion of the Kobe earthquake in Japan on January 17, 1995, is used as earthquake excitation. The time history of displacements and accelerations and frequency responses of the both uncontrolled and controlled cases of the crane structure and control force are obtained. Performance of the designed controller is compared with the classical fuzzy logic controller (FLC). Comparison of the STFLPIDC and FLC in frequency and time domain is presented to evaluate the effect of performance of the controllers. Simulations with the STFLPIDC show better seismic performance than classical FLC. Besides, the robustness of the STFLPIDC was checked through the change in rigidity parameters. It is revealed that using designed controller and active vibration control system causes suppression of the earthquake-induced vibration.