This paper focuses on the adaptive funnel control of a flexible exoskeleton joint based on the singular perturbation method. The singular perturbation is used to find the asymptotic solution of a differential equation by decomposing the system into two subsystems. For the fast subsystem, a torque-feedback-based subcontroller is proposed to ensure the suppression of flexible vibration. For the remaining slow subsystem, an improved funnel error transformation is introduced and integrated into the controller design to achieve a specified tracking error performance. Fuzzy logic systems are employed to deal with the nonlinear uncertainties, and an adaptive fuzzy funnel controller is constructed by backstepping method. The simulation results verify the feasibility of the proposed control scheme.