The estimation of the fissile material production from 5 MWe Yong-byon graphite-moderated reactor is important to evaluate North Korea’s capability to produce nuclear weapons. In this work, the amount of fissile material according to each operating period of the Yong-byon graphite-moderated reactor were estimated using MCNP6 and SCALE6 core modeling, based on the operation histories and the core design of the reactor given in the open literatures. Furthermore, inventories of the Weapon-Grade (WG) plutonium were estimated and the two results of MCNP6 and SCALE6 calculation were compared. In addition, variables not provided in the open literatures: fuel rod rearrangement, boron contamination change, power change, and graphite moderator density change, were used for estimating production of fissile materials. Also, the estimated plutonium production for each variable were compared with the expected mass of plutonium according to the operation records of the Yong-byon graphite-moderated reactor published by Heckers et al. The results from SCALE6 and MCNP6 show that the difference in WG plutonium production for each variable is within 1% at the longest operating time before removing spent fuel. In addition, it was confirmed that the values calculated by SCALE6 and MCNP6 were in the range of the total amount of plutonium produced from 1986 to 2015 during the 5 MWe reactor operation period estimated by Albright.