A new intelligent algorithm is proposed in this paper to identify the high impedance faults (HIF) in distribution systems. After a close analysis on the S transform (ST) and its outputs specifications, all amplitude and phase information of the input signal in both time and frequency domains are extracted. ST output information can be provided by some curves. Then, to quantify the ST output information, four numerical indices named as total harmonic distortion (THD), even harmonic energy (EHE), variation coefficient (VC) and phase difference (PD) are extracted from the ST output curves. Each of the indices represents one of the amplitude or phase information of the signal in time or frequency domains. The numerical indices are used as the inputs of the fuzzy system. Using fuzzy system and its inputs, the HIF is identified from other distribution systems such as the normal situation, load switching, capacitor switching and transformer inrush current. Simulation results show that in the 30dB noisy environment, the accuracy of the proposed algorithm is higher than 98.5%. Using the parameter PD, the algorithm implementation time is near 0.02 seconds. Test signals are extracted from a real 20kV network simulated in PSCAD software. Results of testing the proposed algorithm show its superior performance in real distribution systems. Having high speed and low computational burden of the proposed algorithm, make it a good choice for applying on the protective relays.