This study presents the comparison of analytical fragility functions obtained from analyses result of spectrum matched to unmatched ground motions expressed in terms of percentage and ratio. Seven random seed earthquake ground motions were matched to United States Nuclear Regulatory Commission (USNRC) specified design response spectrum to carry out time history analyses of a base-isolated nuclear power plant structure. Fragility functions were estimated using the maximum likelihood method from the obtained responses for the selected ground motions. As anticipated the seismic responses obtained using matched time series were higher than unmatched time series which finally led a higher mean. Standard deviation for both cases were compared and for spectrum matched case smaller result were noticed.