Modeling the run-in of a pebble-bed reactor (PBR) can be challenging as a result of changes in the power, fuel type, and temperatures that occur throughout the run-in period. Previous work utilized high-fidelity neutronics simulations or lower-fidelity coupled neutronics/thermal-hydraulics models to capture the general characteristics of the run-in process. The present work employs high-fidelity neutronics simulations (using Serpent) coupled with thermal-hydraulics simulations (using Griffin–Pronghorn) to capture the thermal feedback present during the run-in and approach to equilibrium for a PBR. Incorporating thermal feedback enables important distinctions to be made about conditions occurring inside the core,as the power distribution, discharge burnup, and isotopic compositions are all affected by the temperature distribution.