To ensure fast dynamics and the stability of multiple distributed generator units (DGUs) in DC microgrids, communication links among the controllers of DGUs are generally adopted. However, those communication channels are vulnerable to cyber-attacks. To alleviate this hassle, a Kalman Filter (KF)-based distributed cyber-attack mitigation strategy, which is highly involved in both primary and secondary control, is proposed in this paper. The KF, as a robust state estimator, is utilized to accurately estimate the authentic terminal voltages and currents of the DGUs. Based on the discrepancies between the estimated and measured parameters of the systems under cyber-attacks, the proposed control can adaptively compensate the attack signals via an adaptive proportional integral (API) controller and a fractional API (FAPI) controller in cyber-attack-mitigation layers. The main advantage of using the proposed control scheme compared to conventional schemes is the fast dynamic response. The simulation results verify this merit by comparing the adopted KF and comparing it with conventional artificial neural networks (ANN), while the experimental results validate that effectiveness of the proposed control and showcase the superiority of the FAPI control in terms of its perfect compensation for different types of cyber-attacks.