This article proposes an advanced nonlinear soil-structure interaction methodology, for the seismic analysis of a nuclear structure. To do so, a study is performed on a nuclear reinforced concrete structure considering the effects of the nonlinearity due to the sliding and rocking at the soil-structure interface, under a Beyond Design Basis Earthquake. A tridimensional numerical model based on the Finite Element Method is developed for the structure and the soil. The model of the structure considers composite materials to describe all the structural members, taking full advantage of the modelling capabilities of the finite element method. The soil layers are modelled assuming their degraded properties due to the propagation of the seismic ground motion. An innovative approach to achieve spectral matching at the surface of the FEM soil model after propagation from the bedrock has been successfully implemented. The seismic analysis on the structure has been performed by considering three hypotheses for the contact between soil and structure: fixed-base, fixed contact and sliding-rocking contact. Insights are provided after comparing floor spectra for the contact approaches assessed in this research, calculated at the systems and components’ locations at the nuclear structure. Finally, a statistical approach for the soil properties allows to study the effects of these uncertainties on the structural response.