This study is performed within the framework of the “High-Performance Advanced Methods and Experimental Investigations for the Safety Evaluation of Generic Small Modular Reactors” (MCSAFER) H2020 European project. The main aim of this project consists of demonstrating the importance of the application of advanced modelling tools in the safety analyses of Small Modular Reactors (SMR). In this work, a comparison between the results of the simulation of the boron dilution sequence using the system code, TRACE, and the advanced modelling tool TRACE/SUBCHANFLOW (SCF) is presented. To do so, a full-plant TRACE model using a 3D modelling approach for the primary side region along with a NuScale core model for the SCF code have been built using the publicly available data of the NuScale SMR. Finally, the obtained results by means of the two different modelling approaches are presented and the comparison show the impact of the usage of the multiscale TRACE/SCF tool on the results of the evolution of the boron dilution transient. As an important conclusion, it should be noted that, although the implementation of the most accurate 3D TRACE components available to model the core in the TRACE standalone version, the modelling of the core region with the SCF code results in a more accurate calculation of the crossflow among fuel assemblies. However, the role played by TRACE in the core inlet boundary conditions is also relevant in the results, so it is worthy to do the effort to model the primary side in detail.