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In this paper, finite element modeling of friction welding of two ASTM A106-B and AISI 4140 dissimilar pipes is investigated. The effect of the friction welding parameters including rotation speed, friction pressure, friction time, forging pressure and forging time on the axial shortening are investigated using a fractional factorial design method. Because of the extreme material deformation, an innovative remeshing technique was scripted in Abaqus CAE to prevent the creation of distorted elements. 27 models were solved and 3 validation experimental tests were carried out. Results showed that increasing the all parameters cause larger axial shortening. Friction pressure with 33.9% had the most effect on the axial shortening. Moreover, an increase in forging pressure and forging time has a limited effect on the axial shortening. After about 2 seconds from the beginning of the welding, the temperature of the interface becomes steady at about 1250°C. The validation tests revealed that the simulation error was about 5.6% which shows a good agreement between the finite element results and the experimental data.