Public school buildings in Peru feature several classrooms in rows, replicating on the second floor, up to 3 stories. The structural system consists of RC frames in the longitudinal direction, and confined masonry walls in the transverse direction, with RC frames in the middle of each classroom. The width of such buildings is 7.8 m, so they are called 780 school modules. Previous studies on the seismic behavior of these buildings have focused on the longitudinal direction, which has suffered important damages in past earthquakes, while the transverse direction has had almost null attention. Furthermore, current Peruvian Codes do not provide clear guidelines for incorporating Soil-Structure Interaction (SSI) into the modeling of structures, particularly nothing is specified concerning confined masonry walls. This study focuses on the seismic behavior of a school building in the direction of the confined masonry walls and assesses the responses when SSI is considered. To achieve this, research related to soil-structure interaction and nonlinear analysis in confined masonry was collected. One 780 school module, 2-story and 3 classrooms per story, located on intermediate soil was selected for study. Four models were prepared, one with a fixed base and three with flexible bases, to consider SSI. The load-displacement capacity curves obtained were used to compare the structural response on the masonry walls. The results show the importance of considering SSI in buildings with confined masonry walls. This study concludes with the need to incorporate SSI in future research on modeling buildings with masonry walls.