© 2015 Informa UK Limited, trading as Taylor & Francis Group. To achieve a significant improvement in the overall performance of a flexible manufacturing system, the scheduling process must consider the interdependencies that exist between the machining and transport systems. However, most works have addressed the scheduling problem as two independent decision making problems, assuming sufficient capacity in the transport system. In this paper, we study the simultaneous scheduling (SS) problem of machines and automated guided vehicles using a timed coloured Petri net (TCPN) approach under two performance objectives; makespan and exit time of the last job. The modelling approach allows the evaluation of all the feasible vehicle assignments as opposed to the traditional dispatching rules and demonstrates the benefits of vehicle-controlled assignments over machine-controlled for certain production scenarios. In contrast with the hierarchical decomposition technique of existing approaches, TCPN is capable of describing the dynamics and evaluating the performance of the SS problem in a single model. Based on TCPN modelling, SS is performed using a hybrid heuristic search algorithm to find optimal or near-optimal schedules by searching through the reachability graph of the TCPN with heuristic functions. Large-sized instances are solved in relatively short computation times, which were a priori unsolvable with conventional search algorithms. The algorithm’s performance is evaluated on a benchmark of 82 test problems. Experimental results indicate that the proposed algorithm performs better than the conventional ones and compares favourably with other approaches.