In this paper, a novel fault‐tolerant control scheme is designed and analyzed for multi‐agent systems (MASs) with incipient faults, disturbances, parameter uncertainties, time delay, and nonlinear terms, and the proposed MAS with switching communication topologies. Firstly, the proposed distributed extended state observer estimates the incipient fault and system states in follower agents, which extends the incipient fault vector to a new system state. Meanwhile, the designed observer considers the output errors of itself and other agents. Further, a state estimation feedback‐based fault‐tolerant controller is constructed, composed of a delay estimator and a non‐delay estimator to guarantee the proposed MASs have good operation performance. Then, some stability analysis conclusions of the MAS with incipient faults, time delay, disturbances, parameter uncertainties, and nonlinear terms are obtained. The proposed results can also be applied to practical systems like the wireless power transfer system. Finally, two simulation results are provided to demonstrate the effectiveness of the proposed fault‐tolerant control technique.