Some studies have shown that a conventional seismic isolation system may suffer from an excessive isolator displacement when subjected to a near-fault earthquake that usually has a long-period velocity pulse waveform. In order to alleviate this problem, a semi-active isolation system (SAIS) with a variable friction damper (VFD) controlled by proposed fuzzy controllers is investigated in this study. By varying the clamping force in the VFD damper, the slip force of the damper applied on the isolation system can be regulated on-line. Moreover, in order to determine the clamping force, four types of simple fuzzy controllers are developed based on the concept of antilock braking systems used in automobiles, and their isolation performances are simulated and compared. In addition, in order to assure a fair comparison, four types of earthquakes, namely far-field, weak near-fault, strong near-fault, extreme near-fault earthquakes, representing a wide variety of ground motions are considered as the ground excitations in the simulation. The numerical result shows that among the four fuzzy controllers proposed, the one that takes the ground velocity as an input variable has the best overall performance. As compared to the uncontrolled passive isolation system, the SAIS system with this controller greatly reduces the structural acceleration and base displacement responses simultaneously in a strong or extreme near-fault earthquake, whereas the controller results in a roughly equal level of acceleration response and a much less base displacement in a far-field or weak near-fault earthquake.