As the System-on-Chip (SoC) complexity increases, hardware/software co-design plays an important role to improve design productivity, reduce time to market, and optimize the overall results. Consequently, there is a high interest in providing rapid system validation in such a paradigm to achieve the aforementioned objectives. There exist in previous works prototyping techniques related to the development phase. FPGA-based prototyping has the benefits of enabling HW/SW integration and system validation after the Register Transfer Level (RTL) implementation is available while virtual platforms provide capabilities to accelerate software development with higher level functional models, e.g. Transaction Level Modeling (TLM). In this paper, we propose a hybrid prototyping methodology which takes advantage of virtual and FPGA-based prototyping in a single framework. We aim to provide a rapid and flexible system validation solution for HW/SW co-design at various stages of development based on the availability of TLM and RTL implementations. The proposed methodology allows online and offline performance analysis and debugging for early feedback in HW/SW architecture exploration. This was evaluated in the experiments with a neural network processor as a case study.