Seismic isolation systems employ structural control that protect both buildings and vibration-sensitive contents from destructive effects of earthquakes. Structural control is divided into three main groups: passive, active, and semi-active. Among them, semi-active isolation systems, which can reduce floor displacements and accelerations concurrently, has gained importance in recent years since they don't require large power or pose stability problems like active ones. However, their seismic performance may vary depending on the variations that may be observed in the mechanical properties of semi-active devices and/or seismic isolators. Uncertainties relating to isolators can arise from variations in geometry, boundary conditions, material behavior, or temperature, or aging whereas those relating to semi-active control devices can be due to thermal changes, inefficiencies in calibrations, manufacturing errors, etc. For a more realistic evaluation of the seismic behavior of semi-active isolated buildings, such uncertainties must be taken into account. Here, the probabilistic behavior of semi-active isolated buildings under historical pulse-like near-fault earthquakes is evaluated in terms of their performance in preserving structural integrity and protecting vibration-sensitive contents considering aforementioned uncertainties via Monte-Carlo simulations of 3-story and 9-story semi-active isolated benchmark buildings. The results are presented in the form of fragility curves and probability of failure profiles.