In this work, Hilbert-Huang Transform (HHT) is applied for fast detection and location of faults using quarter cycle post fault current information, measured at the secondary of the substation transformer. Empirical Mode Decomposition (EMD) is carried out over a moving window to obtain first level residue, on which Hilbert Transform (HT) is applied in order to obtain the instantaneous attributes. Standard deviations of instantaneous frequency (SDIF), amplitude (SDIA) and average value of residue (AVR) are obtained for computing fault location indices. A tree like logic flow is implemented by comparing these indices with thresholds to identify the zone of fault and subsequently the exact fault location. The proposed algorithm has been implemented for IEEE 13 bus distribution system using MATLAB. Various case studies involving changes in fault type, fault incidence angle, bus location, fault resistance have been carried out in order to establish the proposed algorithm. It has also been established that the protection algorithm is not affected by non faulty transients such as switching of compensating equipment. © 2019 IEEE.