Structural dynamics simulations are often faced with challenges arising from unknown boundary conditions, leading to considerable prediction uncertainties. Direct measurement of these boundary conditions can be impractical for certain mounting scenarios, such as joints or screw connections. In addition, conventional inverse methods face limitations in integrating measured data and solving inverse problems when the forward model is computationally expensive. In this study, we explore the potential of physics-informed neural networks that incorporate the residual of a partial differential equation into the loss function of a neural network to ensure physically consistent predictions. We train the neural network using noisy boundary displacement data of a structure from a finite element reference solution. The network learns to predict the displacement field within the structure while satisfying the Navier–Lamé equations in the frequency domain. Our results show that physics-informed neural networks accurately predict the displacement field within a three-dimensional structure using only boundary training data. Additionally, differentiating the trained network allows precise characterization of previously unknown boundary conditions and facilitates the assessment of non-measurable quantities, such as the stress tensor.