In this paper, we deal with a decentralized control scheme with input compensation form for gantry crane systems. By considering the gantry cranes characteristics, the system is decentralized into two subsystems, the travelling and swaying subsystem and the hoisting subsystem. For decentralizing the system, a simple algorithm is proposed using the observability canonical form. The decentralized subsystems include unknown inputs that one coupled with other subsystems and actuator failures. These unknown input and actuator failures are estimated by using PI observation techniques. And those estimated values are used to construct an input compensation form. Finally, the proposed decentralized control scheme for the gantry crane systems is verified by crane simulation.