In the finite element method framework, a fluid–structure formulation is developed by coupling an Eulerian fixed-mesh fluid approach with a Lagrangian deforming-mesh description for a flexible solid. The coupled formulation is solved using a staggered scheme during time. For the fluid solution stage, the solid walls are considered as a time-variable internal boundary. The velocity and pressure fields are obtained by solving the weak form of the fluid dynamic equations in which the solid velocity is imposed on the internal boundary via a penalization term. For the solid solution stage, the displacement field is obtained by solving the discrete solid dynamic equations which consider traction forces computed by integrating pressures and viscous stresses on the nodes belonging to the solid walls. This novel technique is firstly applied to analyze a flexible splitter under the shedding of a flow past square cylinder due to this problem is considered as a benchmark in the literature. The present solutions agree with those computed using body-fitted techniques, thus validating the proposal. Secondly, flexible splitter motions under the shedding of flow past cylinders with different cross-sections and splitter lengths are comprehensively studied. Overall, the computed results confirmed that the hydrodynamic coefficients on the cylinders were reduced because of the presence of the splitter.