Base isolation can significantly increase the seismic performance of structures. Nevertheless, different design options complying with current building code requirements can result in base-isolated structures with different seismic performance levels. Moreover, seismic loss quantification is generally performed at the end of the design process, typically for assessment purposes. This paper presents a methodology for seismically design low-rise base-isolated structures to achieve a predefined level of earthquake-induced direct losses, requiring no design iteration. The procedure is enabled by a Gaussian process-based surrogate model that predicts the seismic demand of equivalent single degree of freedom systems (i.e., the probability distribution of peak horizontal displacements and accelerations conditional on different ground-motion intensity levels). Such an approach – combined with simplified loss models for the base-isolated system and the structural and non-structural components of the superstructure - allows mapping a range of structural configurations to their resulting loss. The designer can select one of the identified combinations of stiffness, strength of the superstructure, and isolator properties that conform with the loss target. Therefore, direct displacement-based design principles and the general theory for the detailing of the isolation system are used. The procedure is applied to a case-study base-isolated essential facility, showing a loss estimate comparable to a benchmark based on refined time history analyses and FEMA P-58 guidelines.