The vibrational response of adhesively bonded joints with and without defects in the adhesive layer is predicted by simulation for the different overlapping lengths in this work. The eigenvalue extraction method (Block Lanczo’s) is employed within the finite element analysis (FEA) framework to predict the modal values of adhesively bonded joints. The numerical analysis has adopted a solid 20-node quadratic brick elements with reduced integration (C3D20R) to predict the realistic values. The predicted eigenvalues of adhesively bonded joints using an FEA solution are compared with published data and verified the accuracy of the FEA model through experimentation considering defective and non-defective joints. Additionally, simulation solutions are predicted for different overlap lengths (i.e., 25, 30, 35 and 40 mm) by changing the boundary conditions, adhesive bond thickness aspect ratio, adherend thickness ratio, defect position, and defect aspect ratio. The geometries of the adhesive and adherend significantly affect vibration responses through the dampening effect and structural weight, enhancing the stiffness. Defect position and geometry have negligible impact on the natural frequency values for all overlapping lengths except when located around the overlapping edges.