The construction of an underground silo structure was the first stage of erecting the Gyeongju low-and-intermediate-level radioactive waste disposal facility. The facility, completed in 2014, has a scale of 100 000 drums and is currently in operation. The underground silo structure, 25 and 50 m in diameter and height, respectively, consists of cylindrical (for storing waste packages) and dome parts. The dome is divided into lower (connected to the operation tunnel) and upper parts. The wall of the underground silo structure is an approximately 1-m-thick reinforced concrete liner. In this study, finite element analysis was performed for each phase of the construction sequence and operation of the underground silo structure. Two-dimensional axial symmetric finite element analysis was implemented using the SMAP-3D program. Three-dimensional finite element analysis was also performed to examine the reliability of the two-dimensional axial symmetric finite element model. The structural behavior of the underground silo structure was predicted, and its structural safety was examined.