The multi-agent-based supply chain network is a dynamic system consisting of multiple subchains connected by information flows, material flows and capital flow, etc. The consensus of multi-agent systems is often applied to the cooperation between subchains and inventory management in supply chain networks. Considering the ubiquitous external disturbances, this paper mainly considers the fixed-time consensus of a stochastic three-echelon multi-agent-based supply chain system. A nonlinear feedback fixed-time control protocol is constructed for ensuring the consensus of the considered supply chain network. Using the stability theory of stochastic differential equations, sufficient conditions for the fixed-time consensus and the upper bound estimation of the settling time are obtained. Finally, the validity of the control protocol and the correctness of the theoretical analysis are revealed by numerical simulation.