The resin injection pultrusion is an automated composite manufacturing method in which the resin is injected in a chamber. The flow and the thermo chemical mechanical (TCM) models have been studied for the pultrusion process to improve the reliability of the final products. Flow models are needed to understand and describe the fiber impregnation, filling time and presence of dry spots or voids. Also pressure field in the injection chamber can be estimated with flow models. TCM models are needed to predict residual stress distributions and to optimize the process conditions. A non-uniform fiber distribution strongly affects the results of both types of models. In this study, different strategies are carried out to implement non-uniform fiber distributions into the models. The cross-sectional image and fiber distribution of a 19×19 mm glass fiber reinforced polyester unidirectional pultruded composite is used. Non-uniform fiber distribution is observed and implemented into the flow model by means of permeability variations. The results of this study are compared with uniform fiber distribution results. In the TCM model, the non-uniform fiber volume content is implemented within different sized patches. The results show that the non-uniform fiber fraction should be taken into account for the process models of composites in order to capture the local process induced stresses and probability of dry spots or voids due to poor fiber impregnation.