The Ebe schooner-brig was built in 1921 and sailed the Mediterranean’s sea for almost forty years, before being dissected into ninety parts to be transported in Milan (Italy). There, the schooner was reassembled and the naval pavilion of the National Museum of Science and Technology was built up all around the ship. After forty years in the museum, the ship presents significant deformations of both the deck and the keel, particularly in correspondence of the external supports. Despite several interventions in the past and a recent restoration, the deformation phenomenon is still worrying, and the understanding of the real cause is lacking from many aspects. Experts have already advanced some hypotheses, often in opposition to one another, and unfortunately, a continuous monitoring of the ship deformation has not been started yet. In the present paper, the schooner structure is modeled with the commercial finite element code Diana, considering a two-dimensional model of the ship cross-section. The obtained results allow for a deeper understanding of the stress-strain field in the schooner, providing a first safety assessment and useful hints for the design of the monitoring and future interventions.