Fluid-Structure Interaction (FSI) simulations have applications to a wide range of engineering areas. One popular technique to solve FSI problems is the Arbitrary Lagrangian-Eulerian (ALE) method. Both academic and industry communities developed codes to implement the ALE method. One of them is Alya, a Finite Element Method (FEM) based code developed in Barcelona Supercomputing Center (BSC). By analyzing the application on a simplified artery case and compared to another commercial code, which is Finite Volume Method (FVM) based, this paper discusses the mathematical background of the solver for domains, and carries out verification work on Alya’s FSI capability. The results show that while both codes provide comparable FSI results, Alya has exhibited better robustness due to its Subgrid Scale (SGS) technique for stabilization of convective term and the subsequent numerical treatments. Thus this code opens the door for more extensive use of higher fidelity finite element based FSI methods in future.