Forward-directivity effects create distinct velocity pulse in the fault-normal direction of near-fault ground motions. It has been shown that this pulse period governs the structural response of fixed base buildings. The present study examines the effects of the near-fault pulse-like ground motions on seismically isolated buildings, considering different effective isolation period to pulse period ratios. Three sets for near-fault ground motions with varying pulse periods are employed to determine the effects of pulse-like ground motions on isolator displacements, superstructure drift ratios, and superstructure load distributions. These effects are categorized as spectral shape and amplification. It is seen that the pulse period forms the spectral shape of records. Spectral acceleration relatively decreases in the short periods and increases in the long periods by enhancing the pulse period. This phenomenon reduces isolator displacement demand for near-fault ground motions with the large and medium pulse periods considering ASCE 7–16 scaling range. An intensity measure parameter is modified to indicate the spectral shape effect of pulse-like records on the isolated buildings. Also, the amplification ratio for the isolator displacement caused by the pulse period is obtained, excluding the spectral shape effect and considering the pulse period to effective isolation period ratio. Further, the R-μ-T relation of the first-floor acceleration, transferred acceleration to the superstructure, is acquired to determine the pulse period effect on superstructures. The results show that the superstructure ductility demand is very sensitive to the pulse period, and the effectiveness of the isolation system considerably decreases by enhancing the pulse period. Also, it is demonstrated that the pulse period governs the lateral load distribution for the superstructure.