Masonry buildings of historical centres are usually organized within aggregates, whose structural performance against seismic actions is challenging to predict and constitutes still an open issue. The SERA—AIMS (Seismic Testing of Adjacent Interacting Masonry Structures) project was developed to provide additional experimental data by testing a half-scale, two-unit stone masonry aggregate subjected to two horizontal components of dynamic excitation. In this context, this paper investigates the reliability of the modelling approach and the assumptions adopted to generate a three-dimensional continuum finite element model. The work involves two stages, namely a blind pre-diction and a post-diction phase, and proposes a series of simulation analyses including a strategy to shorten the actual records and save computation costs. The study was performed to investigate the extent of uncertainty in modelling for such masonry aggregates in relation to the experimental outcomes. Pre-diction results were proven to be not accurate in terms of predicted displacements and damage patterns. The upgrades introduced for the post-diction analyses, including the calibration of the elastic modulus and the introduction of a non-linear interface between the two units, allowed to improve the outcomes, with reasonable results in terms of predicted base shear force, displacements along Y-direction and damage pattern for the non-linear stage. The overall approach showed to be appropriate for the structural analysis of existing masonry aggregates, but the accurate modelling of this type of structure remains challenging due to the high level of uncertainties.