A new Data Acquisition (DAQ) sub-system for gamma-ray diagnostics was developed for Joint European Torus (JET). The system is based on the ATCA platform and is able to sample up to 400 MSPS with 14-bit resolution. This DAQ is used for gamma-ray diagnostics dedicated to the study of fast ions in fusion tokamak plasma experiments. The present work describes the development of pulse processing algorithms used to extract the pulse parameters from the DAQ free running ADC data streams. These algorithms are divided in three main functional blocks, namely, advanced triggering and segmentation, segmentation validation and finally, peak height analysis (PHA) and pile-up rejection (PUR). The developed algorithms perform the pulse segmentation, shaping and validation according to the noise level and characteristics of the digitized signal. Shaping is performed through a reconfigurable trapezoidal filter in order to optimize the spectral resolution with the required throughputs and a comprehensive study of this parameterization is presented. Calibration procedures are mandatory for an efficient real time application and its implementation in the FPGA is discussed and explained. The presented and discussed results refer to the analysis of the JET pulse files obtained during the recent campaigns where a spectral resolution of 4.5% for the 137Cs energy peak at 662 keV was achieved through FPGA real time processing. Results of high gamma-ray reaction rates experiments performed outside JET are also presented.