We have developed a tightly coupled multiphysics simulation tool for the pebble bed reactor (PBR) concept, a specific type of very high temperature gas-cooled reactor. The simulation tool PRONGHORN takes advantage of the Multiphysics Object-Oriented Simulation Environment library and is capable of solving multidimensional thermal-fluid and neutronics problems implicitly with a Newton-based approach. Expensive Jacobian matrix formation is alleviated via the Jacobian-free Newton-Krylov method, and physics-based preconditioning is applied to minimize Krylov iterations. Motivation for the work is provided via analysis and numerical experiments on simpler multiphysics reactor models. We then provide detail of the physical models and numerical methods in PRONGHORN. Finally, PRONGHORN's algorithmic capability is demonstrated on a number of PBR test cases.