In this study, neutronic performances of the fertile thorium and natural uranium were studied in a Gas Turbine-Modular Helium Reactor using Weapons Grade Plutonium as fissile fuel. In the first step of the calculation procedure, a series of neutronic calculations were made in order to find the proper mixture ratios for these fertile fuel mixtures by using MCNP5 with ENDF/B-VI cross-section library. After the determination of these mixture ratios, in order to compare these fuel mixtures, time dependent neutronic calculations were made by using Monteburns 2.0 with MCNP5 and Origen 2.2. According to the results obtained, different parameters (operation time, burnup value, fissile isotope production, etc.) were compared. Results of the first step showed that, in order to reach the reference k(eff) value, 690.6 kg more fissile isotope was used in natural uranium mixture than the thorium mixture. In the second step of this study, time dependent calculations showed that for the natural uranium mixture, operation time and burnup values were found as 1935 days and 177.76 GWd/MTU, respectively, while these values for thorium mixture were 1925 days and 153.95 GWd/MTU. (C) 2015 Elsevier Ltd. All rights reserved.