Airspace companies regularly incorporate state-of-the-art automation technologies into their aircraft assembly systems to reduce lead times and manufacturing costs and improve product quality in their assembly plants. Rapid advances in assembly automation, robotics, material handling, measurement in the assembly processes, and systematic design methodologies require constant consideration of new applications and technologies in assembly systems’ design studies for airplane structures such as fuselage panels. Such a design study is performed in this study to enable the formation of an automated, reconfigurable and robotic fuselage panel final assembly system. The authors’ extensive review of the literature and catalogs reveals that stringer positioning robots, 3D projection devices for fastener position controls on the panels, reconfigurable fixtures for holding the panels, mobile refill friction stir spot joining robots to assemble clips to frames, robotic measurement systems, and modular crane for material handling can be used as state-of-the-art automation technologies in an automated and reconfigurable fuselage panel final assembly system. The proposed automated, reconfigurable, and robotic fuselage panel final assembly system provides an increase in its performance of adaptation level to the changes in the panel types, customers’ order quantities, and suppliers’ and customers’ delivery dates.