The paper considers the iterative learning control (ILC) design problem of a network system under changing operating mode of subsystems (agents) and configuration of information network. The network system consists of identical agents, which are discrete linear dynamic plants operating in a repetitive mode. The operating modes of agents depend on their parameters and the reference trajectory, which must be tracked with required accuracy at output of system. The configurations of information network define the group of functioning agents and the type of information exchange between them. The mode and the configuration change takes place in accordance with certain external rules. The control design is based on the divergent method of the vector Lyapunov function. For reducing the transient error caused by the mode change and the connection of new agents, a special rule for switching the ILC law is proposed. The results of modeling the obtained control law for a group of manipulators with flexible link are presented.