Fast Fourier Transform (FFT) is generally implemented on reconfigurable hardware in several signal processing or digital communication applications. It can be considered the most time and resource consuming operations due to the need of complex operations. The main of this manuscript is to investigate the contribution of High Level Synthesis (HLS) techniques on the implementation of real time FFT algorithms using field programmable gate arrays (FPGAs). In particular, this study focuses on communication systems incorporating filter-based-multicarrier modulations (FBMC), a promising candidate for the 5G technology. In order to evaluate the contribution of HLS, we implemented and tested various combinations such as: 8 and 16 points radix-2 and radix-4 FFT using finite precision, HLS tools and HDL while prompting parallelization, pipelining and hardware reuse architectures.