|The University of Washington (UW) clinical neutron therapy system (CNTS) has been used in the fast neutron therapy of cancer since 1984. Fast neutron therapy has proven to have better clinical outcomes, when compared to traditional X-ray therapy, in the treatment of tumor types such as salivary gland tumors, locally advanced prostate cancer, and high risk soft tissue sarcomas. However, because of the high-toxicity (except for a few tumor sites) compared to X-ray therapy, the high-cost of building a fast neutron facility, and rapid advances in X-ray therapy, the continued advancement of fast neutron therapy stalled. This has also limited the development of treatment planning software specific to neutron therapy. The CNTS uses a photon model in the treatment planning software Pinnacle, fitted with CNTS measurements for treatment planning. This model suffers when the field shape is highly irregular, wedged, or off the central axis. To mitigate these problems, a MCNP6 model of the UW CNTS was developed to simulate the neutron dosimetry and relative biological effectiveness (RBE) effects of the beam. Simulations of tissue maximum ratios, output factors, and wedge factors matched measurements within 5.2% for all data points in square fields with water or a model of an IC-17 ion chamber as the tally volume, and within 6.8% for off-axis irregular fields. This is an improvement over Pinnacle agreement with measurements. The RBE endpoints examined were the induction of deoxyribonucleic acid (DNA) double-strand breaks (DSB),single-strand breaks (SSB), and DNA base damage (Bd) using the MCDS software. The RBEDSB under aerobic conditions ranges from 2.5 to 3.4 for monoenergetic neutrons with energies from 2 keV to 100 MeV in a cell layer in air and 1.3 to 3.2 when the cell is at a depth of 1.7 cm in water. For the CNTS fast neutron beam model, the RBEDSB in water under aerobic conditions is 1.65±0.05 (RBESSB+Bd = 0.09±0.02), and 2.65±0.15 (RBE SSB+Bd = 0.16±0.02) under anoxic conditions, at depths greater than 2 millimeters. The MCNP6 dosimetry and RBE model ensures maximum benefit from further development of advanced treatment methods such as intensity modulated neutron therapy.