Component failures can lead to performance degradation or even failure in multi-agent systems, thus necessitating the development of fault diagnosis methods. Addressing the distributed fault diagnosis problem in a class of partial differential multi-agent systems with actuators, a fault estimator is designed under the introduction of virtual faults to the agents. A P-type iterative learning control protocol is formulated based on the residual signals, aiming to adjust the introduced virtual faults. Through rigorous mathematical analysis utilizing contraction mapping and the Bellman–Gronwall lemma, sufficient conditions for the convergence of this protocol are derived. The results indicate that the learning protocol ensures the tracking of virtual faults to actual faults, thereby facilitating fault diagnosis for the systems. Finally, the effectiveness of the learning protocol is validated through numerical simulation.