A technique is developed to identify in-situ the tensile force in tie-rods which are used in ancient monumental masonry buildings to eliminate the lateral load exercised by the vaults and arcs. The technique is based on a frequency-based identification method that allows to minimize the measurement error and that is of simple execution. In particular, the first natural frequencies of the tie-rods are experimentally identified by measuring the frequency response functions (FRFs) with instrumented hammer excitation; four to six natural frequencies can be easily identified with a simple test. Then, a numerical model, based on the Rayleigh–Ritz method, is developed for the axially loaded tie-rod by using the Timoshenko beam theory retaining shear deformation and rotary inertia. Non-uniform section of the rod is considered since this is often the case for hand-made tie-rods in old buildings. The part of the tie-rod inserted inside the masonry wall is also modeled and a simple support is assumed at the extremities inside the walls. The constraints given to the part of the tie-rod inserted inside the masonry structure are assumed to be elastic foundations. The tensile force and the stiffness of the foundation are the unknowns. In some cases, the length of the rod inside the masonry wall can be also assumed as unknown. The numerical model is used to calculate the natural frequencies for a given set of unknowns. Then, a weighted difference between the calculated and identified natural frequencies is calculated and this difference is minimized in order to identify the unknowns, and in particular the tensile force. An estimation of the error in the identification of the force is given. The technique has been tested on five tie-rods at the ground floor of the famous castle of Fontanellato, Italy.