Functional electrical stimulation (FES) is often used, typically in an open-loop manner, to restore paralyzed motor function for daily living activities. Several feedback control strategies have been developed to improve the performance and usability of FES-evoked movement. However, most of them have been position controllers, while the control strategy for human movement has been known as impedance modulation. Moreover, few studies have attempted to use antagonistic co-contraction for FES feedback control despite its expected benefits, such as enhanced stability and performance and better rehabilitation outcome. In this paper, we propose a robust impedance controller for FES that can adjust the intrinsic joint stiffness using co-contraction. It consists of an impedance control law based on time-delay estimation to compensate for the nonlinear uncertain joint dynamics and an antagonistic muscle co-contraction allocator to address the intrinsic joint stiffness caused by the co-contraction. The proposed controller was implemented on the ankle joints of five healthy subjects to simulate a standing balance situation. The results verified that the proposed controller can achieve desired impedance accurately by adjusting the intrinsic stiffness that stems from the change in the amount of co-contraction (up to 48.4% better impedance achievement with high desired stiffness).