Pultrusion is a continuous and cost-effective process for a production of composite structural components with a constant cross-sectional area. This technological process could be made more effective applying instead of conventional heaters a high frequency electro-magnetic energy source characterized by the fast, instantaneous, non-contact and volumetric heating. To provide better understanding of the microwave assisted pultrusion process, to support the pultrusion tooling design and process control, new simulation methodology consisting of two sub-models has been developed. Each of them is constructed by using the general-purpose FE software that results in considerable savings in development time and costs, and also makes available various modeling features of the FE package. In the first step the electromagnetic sub-model is used to evaluate the electric field distribution by solving the Maxwell’s equations with the COMSOL Multiphysics. It is necessary to note that in this sub-model the transport phenomena is neglected since an influence of the pull speed of the processing material on the electric field distribution is negligible. The objective of simulations is to find the microwave field as homogeneous as possible inside the cured composite profile in the ceramic inlet. In the second step an absorption energy field in the composite material determined with the electromagnetic sub-model is used as a heating source in the pultrusion process modeled with the thermo-chemical sub-model. This simulation procedure is developed in ANSYS Mechanical environment and based on the mixed time integration scheme and nodal control volumes method to decouple the coupled energy and species equations. To demonstrate an application of the developed methodology for the design of technological process, the microwave assisted pultrusion of the cylindrical rod made of glass fibersUnifilo 4800 tex and polyester resin POLRES 305BV has been investigated.