This paper describes the design and implementation of an experimental system created to evaluate the performance of channel estimation and equalisation for spectrally efficient frequency division multiplexing (SEFDM) systems in which higher spectral efficiency compared to conventional orthogonal frequency division multiplexing (OFDM) is achieved by violating the orthogonality of its subcarriers. This work proposes a new frequency-domain channel estimation and equalisation method, then investigates the employment of both OFDM and SEFDM pilot symbols for channel estimation to find channel state information (CSI). It is experimentally shown that the new method offers a reduction in the computational complexity compared to conventional time-domain estimation and equalisation for SEFDM systems with a similar system performance. The design of the baseband signal generation and signal detection using IFFT and FFT structure implemented using LabVIEW communication design suite is described in detail together with the baseband design of the system used to effect signal synchronisation and channel estimation and equalisation.