This paper presents an optimization method on the real-time decoupling control for the TRMS system. It can be stated that TRMS has a complex structure due to its nonlinear structure, cross-couplings, two inputs and two outputs. Despite its complex structure, the TRMS is widely preferred in control applications as it allows to test the controller performances. The pitch and yaw position control in TRMS has been investigated in many studies, but its decoupling control has only been discussed in a limited number of studies. In this study, the real-time decoupling control of the TRMS was performed using fractional order PID. A Genetic Algorithm based optimization method was used for determining the parameters of the fractional order PID controller. The conventional PID was compared with the fractional order PID, and the results showed that the decoupling control of the TRMS using the fractional order PID was more successful. The method applied offers a highly effective control in real-time decoupling control of the TRMS.