The Indirect Symmetrical Phase Shift Transformer (ISPST) stands out from a power transformer due to its combination of electrically connected and magnetically coupled circuits. Hence in this work, an intelligent differential protection algorithm, based on Discrete Wavelet Transform (DWT) and Chebyshev Neural Network (ChNN), is proposed as main classifier to discriminate internal fault and inrush. Half cycle thee phase post fault differential current is considered for the proposed algorithm. PSCAD/EMTDC software is utilized to simulate different operating conditions of ISPST, resulting in the simulation of a significant amount of internal faults and inrush cases. The algorithm under consideration has undergone extensive evaluation across numerous cases, resulting in an accuracy rate exceeding 99%. The results indicate that the classifier based on DWT - ChNN yields extremely promising results, even when dealing with a noisy signal, current transformer (CT) saturation, and varying ISPST ratings. Superiority of the proposed algorithm is also compared with Multilayer Perceptron (MLP), Radial Basis Function Neural Network (RBFNN) and Probabilistic Neural Network (PNN) based approaches under the same conditions and it is found that proposed classifier is the most efficient and rapid among all alternative classifiers for the differential protection scheme of an ISPST under the considered conditions.