Abstract Most of finite element model updating techniques do not employ damping matrices and hence, cannot be used for accurate prediction of complex frequency response functions (FRFs). In this paper, damped finite element model updating procedure is proposed and tested with the objective that the damped finite element updated model is able to predict the measured FRFs accurately. The proposed damped updating procedure is a two-step procedure. In the first step, mass and stiffness matrices are updated using FRF data and in the second step, damping matrix is identified using updated mass and stiffness matrices that are obtained in the previous step. The effectiveness of the proposed procedure is demonstrated by numerical examples as well as by actual experimental data. Firstly, a study is performed using a numerical simulation based on fixed–fixed beam structure with non-proportional viscous damping model. The numerical study is followed by case involving actual measured data for the case of F-shaped test structure. The results have shown that the proposed procedure can be used for accurate prediction of the complex FRFs.