This paper presents a FOPID tuning method for disturbance reject control by using multi-objective BB-BC optimization algorithm. Proposed method allows multi-objective optimization of set-point performance and disturbance rejection performances of FOPID control system. The objective function to be minimized is composed of the weighted sum of MSE for set-point performance and RDR for disturbance rejection improvement. The proposed optimization performs maximization of RDR and minimization of MSE and it can deal with the tradeoff between RDR performance and step-point performance. Application of the method is shown for auto tuning of FOPID controller that is employed for control of TRMS model. We observed that low-frequency RDR indices can be used to improve disturbance rejection performance in multi-objective controller tuning problems. Particularly, for flight control application, disturbance reject control is very substantial to robust performance of propulsion systems.