The Carbon Hydrogen Anti-Neutrino Detector with a Lithium Enhanced Raghavan optical lattice (CHANDLER) detector is an innovative detector design that is able to detect electron antineutrinos from operating nuclear reactors from their inverse beta decay (IBD) interactions within its lattice. High-energy neutrons from cosmic rays can leave a similar signature. In an effort to determine the quenching factor of CHANDLER to high-energy neutron events, a prototype of the system, the MicroCHANDLER detector, has been deployed at the Triangle Universities Nuclear Laboratory (TUNL) to perform experiments using TUNL’s Tandem Van de Graaf accelerator to accelerate deuterium ions to produce high-energy, cosmic-ray–like neutrons in a tritiated-titanium target. The goal of the campaign was to determine the proton quenching factor of the scintillator used in the detector. This paper discusses the Monte Carlo modeling and analysis performed using the MCNP6.1.0 code system. The main goal of the work is to determine the time and space of neutron energy deposition signatures in the detector lattice as a function of the deuterium ion beam energy. In addition, the variation of the response in the presence of a polyethylene shield between the neutron source and the detector is investigated. The findings from this analysis will then be employed to improve the signal-to-noise ratio of CHANDLER by discriminating high-energy neutron- induced events from the IBD events.