The recently proposed independently controlled multiple output flyback converter (ICMOFC) scheme utilizes gallium nitride (GaN) switches with negative gate turn OFF voltage to improve cross-regulation. A cross-coupling exists in such a multiple-input multiple-output control system, which affects converter\'s dynamic performance at high closed-loop bandwidths. Conventional feedback controllers without decoupling control loops lead to lower bandwidth. To address this issue, this digest delineates a methodology for decoupled controller design for the ICMOFC scheme to attain fast transient response. The effect of right half-plane zero of the plant transfer function is also addressed in the suggested decoupled controller. Simulation and experimental results for 40 W two-output flyback converter are provided to validate the suggested control scheme.