The paper deals with development of a methodology for mechatronic system design using state-of-the-art model-based system engineering methods. A simple flexible robotic arm is considered as a benchmark problem for the evaluation of various techniques used in the phases of modelling, analysis, control system design, validation, and implementation. The flexible nature of the mechanical structure introduces inherently oscillatory dynamics in the target bandwidth range, which complicates all the above-mentioned design steps. This paper demonstrates the process of deriving a complex nonlinear model of the flexible arm setup. An initial idea about the plant dynamics is acquired from analytical modelling using the Euler–Bernoulli beam theory. A more thorough understanding is subsequently acquired from finite element analysis. Linearisation and order reduction are the next steps necessary for the derivation of a simplified control-relevant model. A time-dependent variable parameter of load mass position is considered and a robust controller is subsequently designed in order to fulfil certain performance criteria for all the admissible plant configurations. This is performed using a recent H-infinity loop shaping method for fixed structure controller design. The results are validated by means of a physical plant, comparing the experimental data with the model predictions.