Rare earth elements (REEs) are widely used in several high-tech modern industries. Quantification of REEs demonstrates a technical challenge that requires the use of special scientific techniques. These techniques commonly introduce uncertainties that may propagate not only during the sample preparation phase but also in subsequent measurement and analysis phases. The Jordan Atomic Energy Commission is starting up a REE investigation program utilizing many of its available physical and chemical analytical capabilities, one of which is the Neutron Activation Analysis Facility (NAAF) at the Jordan Research and Training Reactor (JRTR). The NAAF provides accurate and relatively quick analytical services for better estimations of REEs in the unknown samples of interest without the need for any chemical processing prior to or after sample activation. In this paper, we present analytical results of routinely conducted instrumental neutron activation analysis (NAA) experiments using REE certified samples. To optimize future NAA investigations, first, a time-dependent Monte Carlo code at the JRTR, named Monte Carlo Code for Advanced Reactor Design and Analysis (McCARD), is herein validated via comparing its calculation results of the activation process against the presented results of the NAA experiments. The certified REE samples were activated in a well-thermalized NAA vertical activation hole within the reactor reflector region. Detailed neutronics and burnup calculations as well as transmutations were performed using McCARD. Ultimately, this study aims to assess the accuracy and reliability of the McCARD calculation models as a part of the effort of setting up a dedicated REE analysis laboratory at the JRTR. This study shows very good agreement between both obtained results—NAA experiment and McCARD calculations—with confidence levels noted to be more than 90% for almost all REE elements.