In this article, an active disturbance rejection control (ADRC) scheme is proposed for the electromagnetic docking of spacecraft in the presence of time-varying delay, fault signals, external disturbances, and elliptical eccentricity. By introducing an auxiliary variable, an intermediate observer (IO) is presented to estimate the relative motion information and the total disturbance resulting from fault signals, unknown mass, external disturbances, and elliptical eccentricity. Then, an ADRC scheme is developed to guarantee that the relative position, relative velocity, and the estimation errors of relative motion information and the total disturbance can all converge into the neighborhood of the equilibrium. With the proposed control scheme, the time-delay factor is fully considered in the controller design to avoid adverse effect, and the uniform ultimate boundedness stability of the entire closed-loop system is analyzed with a rigorous theoretical proof. In comparison to conventional ADRC and other state-of-the-art schemes, the proposed ADRC scheme has several advantages, e.g., high accuracy, strong robustness, and requires no prior knowledge of the fault, time-varying delay and states information due to IO-based relative motion information and total disturbance estimations. Finally, numerical simulations are performed to show the effectiveness of the proposed control scheme.