Drones have become an advanced supply chain implementation instrument, especially in connecting warehouses to outlet points or even individual customers. However, their potential application in an intra-logistics framework has not been studied, let alone explored so far. Modeling and simulations in virtual environments can help explore and evaluate the opportunities for practical and profitable applications of drones in manufacturing systems. This paper considers use of drones in replacing or supplementing industrial robots, transportation systems and humans in factories, especially regarding agile manufacturing under the requirements of flexibility, reconfigurability and collaboration. Currently available drone technology regarding positioning, navigation and communication is examined in order to define possible individual tasks and general operations that they can perform, as well as pertinent limitations. A typical scenario of a flexible manufacturing system is simulated and conceptually presented for discussing drone integration and missing links. The main issues refer to mechanical integration with machinery and parts, information integration in the manufacturing system, especially in an Industrial Internet of Things direction, scheduling and collaboration with humans and robots including safety.