The present study investigates the effect of earthquake sequences on the response of reinforced concrete hilly buildings having typical configurations, that is, stepback and split-foundation, with three different story ratios. A set of 30 as-recorded mainshock-aftershock sequence of earthquake ground motions is considered for this study. Mainshock acceleration time histories are scaled at two distinct intensity levels to obtain the mainshock-damaged building. These mainshock-damaged hilly buildings are then subjected to aftershocks. A comparative study is performed for various response quantities, such as peak interstory drift ratio, peak floor acceleration, and peak roof displacement of undamaged and mainshock-damaged buildings under aftershocks. Further, fragility analysis is carried out to study the effect of aftershocks on undamaged and mainshock-damaged hilly buildings. Subsequently, component-wise seismic loss estimation due to damage in the non-structural and structural components is performed. It is concluded from the study that the building components that contribute maximum to the expected repair cost ratio vary with respect to the intensity of the aftershocks. Also, the estimated seismic loss is higher in mainshock-damaged split-foundation buildings in comparison to stepback buildings.