In the high-temperature reactor design, it is common practice to leave gaps between the graphite blocks of the reflectors to accommodate thermal dilatation and material swelling, as well as to provide an additional cooling source during operation. These gaps give rise to bypass flows entering the reactor core. The bypass flows can change friction factors and heat exchange coefficients obtained in the bulk of the pebble bed. In this paper, a coupled computational fluid dynamics–discrete element method (CFD-DEM) model is proposed. In this model, the pebbles are resolved by the CFD grid and the turbulent field is partially captured using a detached eddy simulation method. The DEM model is first validated against empirical correlations for the packing of the pebbles, and the coupled model is then tested against thermal measurements in the SANA experiment. Then the model is used to perform three-dimensional studies of the effects of the bypass flows in a representative pebble bed configuration. It is determined that the effect of cross flows can be approximately bounded to the first two layers of pebbles next to the reflector wall. Additionally, an increase of ~12% in the Nusselt number in the pebbles next to the reflector is predicted, with a maximum local increase in the pebble of ~100%.