This paper presents a design for a high-speed digital prototype system for discriminating fast neutrons, thermal neutrons, and γ-rays. The system uses a stilbene–⁶Li glass composite scintillator with excellent pulse shape discrimination (PSD) properties as the neutron detector. The PSD performance was investigated at different sampling rates, revealing stable performance at rates above 250 MSPS. The system core is a high-speed acquisition board based on the AD9434 analog-to-digital converter (ADC) and the ZYNQ7020 field-programmable gate array (FPGA), which acquires detector signals and implements real-time algorithms. The system was energy-calibrated with ²²Na, ¹³⁷Cs, and ⁶⁰Co γ-ray sources and evaluated in a n–γ mixed field. Under an ²⁴¹Am–Be neutron source, the system achieved Figure of Merit (FOM) values of 1.26 for fast neutron/γ, 2.18 for fast neutron/thermal neutron, and 3.25 for γ/thermal neutron discrimination above the 50 keVee electron equivalent energy threshold. These results are consistent with the analysis of down-sampled data from a DT-5730 digitizer, confirming that the system meets its design objectives. Additionally, the measured false alarm rates (FAR) were 0.33% for ⁶⁰Co, 0.34% for ¹³⁷Cs, and 0.26% for ²²Na. This system integrates waveform discrimination and energy spectrum measurement capabilities, providing a high-performance, cost-effective electronic solution for high-speed signal acquisition and real-time processing in novel composite scintillator neutron detectors.