In nuclear power plants, there may happen local wall-thinning on the inner surface of a pipe due to the flow of coolant flowing inside the pipe. Pulsed eddy current testing (pulsed ECT) technology is developed in recent years. Because of its rich frequency components and applicability of large electric current, a pulsed ECT method may show promising capability of detecting and evaluating the defect in the deep region of the material. The aim of this study is to discuss the feasibility of detection and evaluation of local wall-thinning of the bottom surface in one thick layer and also in the lower layer of two-layer structure pipe using a pulsed ECT method. Concerning the large thickness of the specimen, a high sensitive flux gate (FG) sensor has been employed and the corresponding differential exciting mode has been developed to efficiently apply the FG sensor. Experimental results show that this FG sensor combined with differential exciting mode could detect a very small defect that is located in a thick specimen while which could not be detected by Hall sensor.