The conventional tube extrusion process has been substituted by porthole die extrusion due to relevant advantages in terms of productivity and quality. However, the porthole die has a complex geometry to be effectively designed; consequently, several studies can be found out in the technical literature based on experimental and finite element analyses of the process. From this point of view, while the experimental investigations entail cost and time increasing, due to the die building complexity, finite element techniques present some drawbacks such as the difficulty to simulate material joining and the loss of accuracy due to the heavy mesh distortion and related remeshing. Therefore, the introduction of new numerical techniques for the analyses of this process could have positive effects. In this paper, the Natural Element Method (NEM) together to the alpha shapes and some extra numerical procedures are used in the simulation of tube extrusion, focusing the attention on the simulation of the welding line in a fully 3D analysis. The obtained results are compared with the finite element and experimental ones, measuring the accuracy of the proposed methodology.