Design/methodology/approach The bearing forces are considered as an external load leading to journal deformation. This deformation is calculated using the finite element method. The pressure distribution producing the bearing force is solved using the finite difference method. The mesh grids in the finite element and finite difference methods are matched for coupling calculation. By iteration, the pressure distribution of the lubricant film at the equilibrium position is determined. Findings Results show that the deformation-induced misalignment has a significant influence on the performance of the bearing when the journal flexibility is taken into account. The parametric study reveals that the misalignment relies on system parameters such as bearing length-diameter ratio and static load. Originality/value The investigation of this work provides a quantification method of misalignment of hydrodynamic bearings considering the elastic deformation of the journal, which assists in the design of bearing in a rotor-bearing system. Peer review The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-10-2023-0337/