In this study, a numerical technique based on the Lattice Boltzmann method is presented to model viscoelastic fluid interaction with complex boundaries which are commonly seen in biological systems and industrial practices. In order to accomplish numerical simulation of viscoelastic fluid flows, the Newtonian part of the momentum equations is solved by the Lattice Boltzmann Method (LBM) and the divergence of the elastic tensor, which is solved by the finite difference method, is added as a force term to the governing equations. The fluid-structure interaction forces are implemented through the Immersed Boundary Method (IBM). The numerical approach is validated for Newtonian and viscoelastic fluid flows in a straight channel, a four-roll mill geometry as well as flow over a stationary and rotating circular cylinder. Then, a numerical simulation of Oldroyd-B fluid flow around a confined elliptical cylinder with different aspect ratios is carried out for the first time. Finally, the present numerical approach is used to simulate a biological problem which is the mucociliary transport process of human respiratory system. The present numerical results are compared with appropriate analytical, numerical and experimental results obtained from the literature.