The aim of this paper is to present a robust and low-cost automatic system for drilling aluminum stacks, as well as an integral methodology for the design of tool trajectories and the control of the drilling process itself. The proposed system employs a high accuracy robotic arm, a commercial spindle head and a specially developed SCADA, which enables it to load tool trajectories designed by using any software application. Furthermore, this SCADA is useful to monitor the main parameters of the drilling process for anticipating problems related to the unexpected tool wear or for a quick response in case of tool collision. A special jig for positioning the stack to be drilled is designed to increase the robot accessibility. In this work, tests are performed for optimizing the cutting parameters of the robotic system in order to maximize the accuracy and the surface finishing of the holes. This analysis is carried out for different tool diameters and taking into account several machining strategies. Finally, a real aeronautical subassembly provided by TIER 1 supplier AERNNOVA is drilled by using the robotic system. The promising results are discussed.