This work presents the design of a decentralized control strategy that allows singularly perturbed multi-agent systems to achieve synchronization with global performance guarantees. The study is mainly motivated by the presence of two features that characterize many physical systems. The first is the complexity in terms of interconnected subsystems and the second is that each subsystem involves processes evolving on different timescales. In the context of interconnected systems, the decentralized control is interesting since it considerably reduces the communication load (and the associated energy) which can be very important when dealing with centralized policies. Therefore, the main difficulty that we have to overcome is that we have to avoid the use of centralized information related to the interconnection network structure. This problem is solved by rewriting the synchronization problem in terms of stabilization of a singularly perturbed uncertain linear system. The singularly perturbed dynamics of subsystems generates theoretical challenges related to the stabilizing controller design but also numerical issues related to the computation of the controller gains. We show that these problems can be solved by decoupling the slow and fast dynamics. Our theoretical developments are illustrated by some numerical examples.