This paper presents a decoupling controller of the missile seeker scan loop with a spin-stabilized platform. A precise seeker motion with respect to the scan command is essential for the higher acquisition probability of the target. As the seeker scan loop is a deeply cross-coupled two input two output system, an accurate pointing or scanning for each axis to the target is very difficult, even though provided with the help of a high performance controller. When a decoupling control is applied to the seeker scan loop, the cross-coupling between two axes can be reduced to a remarkable amount. As a low order of controller is required for the real time operation, a PI controller with decoupling filter is suggested and compared with other controllers. A linearized dynamic model of seeker scan loop is used and validated through the comparison of experimental results of step responses.