This paper presents a distributed integrated fault diagnosis and accommodation scheme for leader‐following formation control of a class of nonlinear uncertain second‐order multi‐agent systems. The fault model under consideration includes both process and actuator faults, which may evolve abruptly or incipiently. The time‐varying leader communicates with a small subset of follower agents, and each follower agent communicates to its directly connected neighbors through a bidirectional network with possibly asymmetric weights. A local fault diagnosis and accommodation component are designed for each agent in the distributed system, which consists of a fault detection and isolation module and a reconfigurable controller module comprised of a baseline controller and two adaptive fault‐tolerant controllers, activated after fault detection and after fault isolation, respectively. By using appropriately the designed Lyapunov functions, the closed‐loop stability and asymptotic convergence properties of the leader‐follower formation are rigorously established under different modes of the fault‐tolerant control system.