In this paper, a suggested design of the fuel pebble and loading pattern in the MIT Modular Pebble Bed HTGR (MPBR) using thorium (232Th) is presented. Using the MCNP5 code model for the MPBR reactor, different compositions of Thorium Low Enriched Uranium (ThLEU) with different Heavy Metal (HM) loading and 235U enrichment were investigated to achieve the maximum thorium utilization with relatively minimum reactivity insertion in case of water ingress accident. Using pure Low Enriched Uranium (LEU) pebbles and ThLEU pebbles with the same HM loading and 235U enrichment, different pebbles loading patterns were studied. One loading pattern was selected to achieve the criticality with enough excess reactivity compensating for the poisoning effect of xenon build-up at the startup of the reactor operation and the negative effect of fuel and reflector temperature coefficients of reactivity. This loading pattern aims also to reduce the radial power peaking in the core and to minimize the axial Power Peaking Factor (PPF) in the central hot channel, with a minimum number of pure LEU fuel batches. A calculation procedure was developed that combines fuel pebble depletion and full core calculations to investigate the impact of a proposed online refueling scheme for the MPBR reactor and to simulate the multicycle refueling mechanism. Using SERPENT 1.1.7, the nuclide concentrations were calculated as a function of pebble burnup for both LEU and ThLEU pebbles. A multicycle online refueling scheme was proposed and the average number of passes required for LEU and ThLEU pebbles to reach their maximum burnup was estimated.