Integration of distributed generation (DG) sources poses new protection challenges in distribution system. The fault current characteristics change due to bidirectional flow of current and unpredictable nature of DG sources. In this work, Stockwell transform based protection scheme has been proposed to detect and classify faults in a distribution network integrated with a solar photo voltaic power plant (SPV). The post fault current transients measured over a moving window at the substation are decomposed using S- Transform to obtain the peak magnitude of second harmonic content which is defined as fault index. This fault index is compared with a threshold (TF) to detect and classify faults. The proposed algorithm has been successfully implemented on IEEE 13 bus system with numerous case studies involving variations of fault incidence angles and fault locations in MATLAB environment. The immunity of the proposed algorithm to switching transients, energization/de-energization of power components and noisy environment has also been established. © 2019 IEEE.