In this article, a novel cooperative secondary voltage/frequency control considering time-varying delays and noises in fading channels is presented for an autonomous alternating current (AC) voltage sourced-based converter (VSC)-based microgrid (MG), including inverter-interfaced distributed generations (DGs). Fading phenomenon makes complex random fluctuations on the voltage and frequency of every DG received from its neighbor DGs. In multi-agent cooperative systems, in addition to the total additive noise and time-variant delay, a multiplicative complex random variable is considered to model the main received signal and its replicas due to multipath propagation. The proposed consensus-based controller is designed by considering fading effects and examines mean square average-consensus considering time-varying delays and uncertainties of the communication system to regulate the voltage and frequency of autonomous AC MGs and provide an accurate real power-sharing. Therefore, by using the proposed protocols, the system sensitivity to fading is decreased, and consequently, the system reliability is increased. Several simulation case studies, such as comparison of the proposed method with previous methods, validate the robustness of our approach against the fading effect.