We present a self-organising, decentralised control method for material flows in networks. The concept applies to networks where time sharing mechanisms between conflicting flows in nodes are required and where a coordination of these local switches on a system-wide level can improve the performance. We show that, under certain assumptions, the control of nodes can be mapped to a network of phase-oscillators. By synchronising these oscillators, the desired global coordination is achieved. We illustrate the method in the example of traffic signal control for road networks. The proposed concept is flexible, adaptive, robust and decentralised. It can be transferred to other queuing networks such as production systems. Our control approach makes use of simple synchronisation principles found in various biological systems in order to obtain collective behaviour from local interactions.