Fueling a plasma reactor by pellet injection is the most efficient method. Production of a solid hydrogen filament using a Twin screw extruder (TSE) is reported to be most stable among various extrusion techniques. The non-Newtonian behavior of solid hydrogen and non-linearities arising due to temperature dependent thermophysical properties in addition to rotation of two intermeshing screws make the flow modelling challenging. In the present study, a non-isothermal and non-Newtonian model has been developed taking into account the temperature and shear rate dependent Herschel Bulkley viscosity model. The ‘slip’ boundary condition has been imposed on the screw surface to account for the localized melting at the screw surface. The highly nonlinear viscous heating term in the energy equation is handled by using evolution scheme. It is important to accurately estimate the viscous dissipation rate which determines the cooling load required and input power. The viscous dissipation rate and developed torque predicted using the CFD model is in close agreement with the experimental available in the literature. The temperature rise due to viscous heating at the clearance gaps and the intermeshing region is found to be 0.6 K higher than that developed in the non-intermeshing region at 4 rpm screw speed for the given extruder dimensions. © 2020 Elsevier B.V.