In this study, a high sampling rate data acquisition system with the ability to provide timestamp, pulse shape information, and waveform simultaneously under a sub megahertz pulse counting rate was developed for radiation diagnostics for magnetic confinement nuclear fusion plasma research. The testing of the data acquisition system under the high pulse counting rate condition using real signals was performed in an accelerator-based deuterium-deuterium fusion neutron source (Fast Neutron Source) at the Japan Atomic Energy Agency. We found that the pulse counts acquired by the system linearly increased up to 6 × 105 cps, and the count loss at 106 cps was estimated to be ~10%. The data acquisition system was applied to deuterium-deuterium neutron profile diagnostics in the deuterium gas operation of a helical-type magnetic confinement plasma device, called the Large Helical Device, to observe the radial profile of neutron emissivity for the first time in a three-dimensional magnetic confinement fusion device. Time-resolved measurements of the deuterium-deuterium fusion emission profile were performed. The experimentally observed radial neutron emission profile was consistent with numerical predictions based on the orbit-following models using experimental data. The data acquisition system was shown to have the desired performance.