A new short time Fourier transformation (STFT) control algorithm is developed for reducing the response of base isolated buildings with variable stiffness isolation systems in near fault earthquakes. The central idea of STFT is to break up the signal into small time segments and Fourier analyze each time segment to ascertain the frequencies that exist in it. For each different time a different spectrum is obtained and the totality of these spectra is the time–frequency distribution. STFT is used to determine the energy spectrum and time–frequency distribution of the earthquake excitation signal. Of particular importance is the tracking of the energy of the earthquake excitation corresponding to the fundamental period of the base isolated building. When the energy of the excitation exceeds a predetermined threshold value the STFT controller varies the stiffness of the isolation system smoothly between minimum and maximum values to achieve response reduction. The main reason for the response reduction is the variation of the fundamental frequency of the base isolated building. Additionally, the STFT control algorithm ensures passivity and energy dissipation during the smooth variation of the stiffness. The STFT algorithm is implemented analytically on a five-story base isolated reinforced concrete building with linear elastomeric isolation bearings and a variable stiffness system located at the isolation level. Several recent near fault earthquakes are considered. It is shown that the controller is effective in reducing the base displacements and interstory drifts without increasing floor accelerations. The novelty of the STFT controller lies in its effective variation of stiffness only a few times to achieve response reduction, which makes it suitable for practical implementation.