In pebble bed reactors (PBRs), pebble flow and coolant flow are highly correlated, and the behavior of each flow is strongly influenced by pebble-coolant interactions. Simulation of both flows in PBRs presents a multiphysics computational challenge because of the strong interplay between the flows. In this paper, a fully coupled multiphysics model is developed and applied to analyze the pebble flow and coolant flow in helium gas-cooled and fluoride salt-cooled PBR designs. A discrete element method is used to simulate the pebble motion to obtain the distribution of pebble density and velocity and the maximum contact stress on each pebble. Computational fluid dynamics is employed to simulate coolant dynamics to obtain the distribution of coolant velocity and pressure. The two methods are fully coupled through the calculation and exchange of pebble-coolant interactions at each time step. Thus, a fully coupled multiphysics computational framework is formulated. A scaled experimental fluoride salt-cooled reactor facility and a full-core helium gas-cooled HTR-10 reactor are simulated. Noticeable changes, such as higher pebble density in the cylindrical core region and more uniform vertical fluid speed profile due to the coupling effect, are observed compared to previous single-phase simulations alone without coupling. These changes suggest that the developed computational framework has higher fidelity compared with previous uncoupled methodology in analyzing pebble flow in PBRs. For the scaled experimental fluorite salt-cooled reactor facility calculation, similar hydraulic loss can be obtained as measured in the University of California, Berkeley, Pebble Recirculation Experiment (PREX), demonstrating the potential of the developed method in thermal-hydraulic analysis for PBRs.