The extrusion of highly filled elastomers is widely used in the automotive industry. In this paper, we numerically study the effect of thixotropy on 2D planar extrudate swell for constant and fluctuating flow rates, as well as the effect of thixotropy on the swell behavior of a 3D rectangular extrudate for a constant flowrate. To this end, we used the Finite Element Method. The state of the network structure in the material is described using a kinetic equation for a structure parameter. Rate and stress-controlled models for this kinetic equation are compared. The effect of thixotropy on extrudate swell is studied by varying the damage and recovery parameters in these models. It was found that thixotropy in general decreases extrudate swell. The stress-controlled approach always predicts a larger swell ratio compared to the rate-controlled approach for the Weissenberg numbers studied in this work. When the damage parameter in the models is increased, a less viscous fluid layer appears near the die wall, which decreases the swell ratio to a value lower than the Newtonian swell ratio. Upon further increasing the damage parameter, the high viscosity core layer becomes very small, leading to an increase in the swell ratio compared to smaller damage parameters, approaching the Newtonian value. The existence of a low-viscosity outer layer and a high-viscosity core in the die have a pronounced effect on the swell ratio for thixotropic fluids.