Embedded systems in the field of digital communications are becoming increasingly diversified and complex. This trend is being confirmed with the emergence of many new application scenarios for mobile communication systems beyond 2020. In this context, rapid prototyping experiences are of high interest for performance validation and proof-of-concept of the diverse proposed communication techniques. In this paper, we present a new design and prototyping experience of an advanced communication system based on filter-bank multi-carrier (FBMC) modulation. This modulation is being studied and considered nowadays by recent research projects as a key enabler for the future flexible 5G air interface. The paper illustrates the complete design and prototyping flow from al-gorithm specification to on-board validation and demonstration. The proposed prototype enables to illustrate and evaluate the performance of this new waveform compared to state-of-the-art OFDM-based systems.