Frequency response functions are the basis for the characterization of modal parameters, which connect system response to the excitation force at the selected points of the structure. Their determination during system operation can be difficult due to the inability to determine the magnitude and the location of excitation force. From this point of view, the methods for identification usually focus on the measurement of transmissibility or the reconstruction of frequency response function through structural modifications. In this work, a new method for frequency response function identification is introduced. By application of so-called pseudo force method, the new formulation enables the indirect identification of operational loads. As more than one pseudo force is usually needed to fully reproduce operational loads the MIMO (Eng. Multi-Input
Multi-Output) method was used for the frequency response function identification. Additionally, the singular value decomposition is proposed to evaluate the dependencies between the pseudo forces and the operating deflection shapes (ODS) to ensure correct magnitudes and phases between different measurement sets. This enabled to design a procedure for the determination of the frequency response functions during system operation without any structural modifications. The efficiency and accuracy of the procedure were verified by the numerical example and validated by the experiment.