The seismic performance of school buildings has been a matter of common interest socially and academically. The structural system of the school buildings is representative of the domestic low-rise reinforced concrete moment resisting frames, which apply extensively infills in their masonry walls. The masonry infilled walls are divided into full masonry infill in the transverse direction and partial masonry infill in the longitudinal direction. The masonry infilled walls are usually not included in structural analysis during the design process, but affect significantly the seismic performance because they behave with surrounding frames simultaneously during earthquakes. Many researchers have studied the effect of the masonry infilled walls, but several issues have been missed such as the increase of asymmetry by adding the full masonry infill, the size of the mean strength of the full masonry infill, and short column effect by the partial masonry infill. The issues were analytically investigated and the results showed that they should be checked at least by nonlinear pushover analysis in the seismic performance evaluation process. The results also confirm the weakness of the guideline of Korean Educational Development Institute where the seismic performance is basically assessed without structural analysis.