The region of Basel is considered one of the most seismically vulnerable in Switzerland: in 1356, a very damaging earthquake hit the city, which nowadays is characterized by a significant concentration of population and economic activities. Hence, the Canton of Basel and the Swiss Federal Office for the Environment have promoted a comprehensive experimental and numerical research program, spanning from the evaluation of the seismic vulnerability of Basel's heritage building stock to the identification of appropriate retrofit strategies. In particular, the experimental program aims at characterizing the mechanical properties of natural stone masonry and investigating the seismic performance of building aggregates typical of the historical city center. To this end, a unidirectional shake-table test was performed on the half-scale model of a natural stone masonry building aggregate, incorporating the main architectural and structural features of existing buildings in Basel's historical center. The aggregate consisted of two three-story units. Double-leaf rubble stone masonry walls, with undressed blocks and river pebbles, constituted the vertical structural elements, while timber floors, simply supported by the transverse walls, provided flexible horizontal diaphragms. The two units were covered by roofs with different truss configurations, pitches, and side-gable wall heights. An incremental, unidirectional dynamic shake-table test was performed up to near-collapse conditions of the specimen, using input ground motions representative of realistic seismic scenarios (natural and induced) for the examined region. The selected records were scaled at different amplitudes, reaching spectral accelerations close to twice those associated with a 475-years return period for the region. The experimental response of the prototype building was also simulated via nonlinear static analysis. The structure was modeled using an equivalent-frame approach with nonlinear macroelements, as implemented in the TREMURI software. The numerical results were compared with the experimental response in terms of pushover and backbone curves and lateral displacement envelopes. The consistency between numerical simulations and experimental results was also verified in terms of damage pattern and activation of damage mechanisms.