Flight control system design typically involves hardware and software development, requiring the definition of both continuous and discrete design parameters. The control surface topology is an example of a discrete optimization problem, whereas the tuning of control system gains is an example of a continuous one. Contemporary design practice classically involves decoupling these two problems, however, they are intrinsically linked; for example, the maximum performance attainable by the control system software is determined by the control system topology employed. The cascaded effect is that no definitive sequential roadmap of development can be established, resulting in the requirement for an iterative framework using dynamic programming or optimization methods. This paper presents a framework for aircraft design together with the Flight Control System Designer Toolkit, and the Computerised Environment for Aircraft Synthesis and Integrated Optimisation Methods. The software platform was developed for the European Framework 6 Program Simulating Stability and Control and integrates both the reliability-driven hardware analysis and the performance-driven software design. A case study is presented, based on the NASA Boeing 747–100 model, in order to demonstrate the potential impact of introducing control design early into the design process and to show the intrinsic nature of the hardware–software FCS problem.