This paper focuses on boundary disturbance rejection control (BDRC) for fractional-order multi-agent systems (FMASs) with reaction diffusion terms. Firstly, based on the output information, the corresponding observer is designed to obtain information about all the agents and the unknown external perturbations. Then, a novel distributed boundary control protocol is designed based on the observed values. Thus, the convergence analysis of the closed-loop system is accomplished through the Mittag-Leffler stability theory and the linear matrix inequality condition. Finally, a simulation example is used to verify the correctness of the results.