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Current seismic performance methodologies such as FEMA P-58 already have the ability to estimate the direct loss and indirect loss of buildings due to earthquakes using performance based earthquake engineering (PBEE). However, earthquake aftershocks, which have the potential to cause additional damage to buildings, are still not considered in these methodologies. On the other hand, previous seismic performance assessment considering aftershocks cannot account for various post-quake decisions (e.g. evacuation, safety evaluation, and repair), and have been based on simplified models which do not have the capacity to simulate many details. In this study, the effects of aftershocks and post-quake decisions on seismic performance are discussed, and an assessment methodology in accordance with other PBEE based methods that also has the ability to consider aftershocks was developed. As a case study, two reinforced concrete frame buildings are adopted for loss estimation using the proposed method. Eighteen near-fault and 60 far-field recorded mainshock-aftershock sequences are employed in the example. The direct loss and indirect loss (downtime and fatality loss) were investigated and show that significant difference may occur in seismic performance when comparing the scenario with and without considering aftershocks.