Fractured formations lead to insufficient contact or loss of contact between the drill bit and rocks, which subsequently causes notable fluctuation in weight-on-bit due to flexible drill strings. This paper presents a robust integrated control design to suppress weight-on-bit fluctuation. First, a finite element drill-string longitudinal model is employed as the basis of control design, which has been verified using actual run data. The integrated controller contains a proportional–integral (PI) controller and a dynamic output feedback controller, dealing with the system’s first-order and high-order dynamics. The dynamic output feedback controller only needs to focus on the system’s high-order dynamics since the controller synthesis is based on the pre-designed PI controller. The controller decreases the flexible mode amplitude from disturbance to the output channel through H-infinity loop shaping, making the closed-loop system less flexible. The numerical results demonstrate that the developed approach can effectively suppress weight-on-bit fluctuation due to drill-string flexibility when drilling in fractured formations.