With the development of industry, the application of linear positioning system has become more and more extensive, ranging from machine tools to optical inspection, laser processing, and robots. With the increase in applications of linear positioning system, linear positioning system has higher and higher requirements for accuracy and environment. Because of errors in assembly and processing of the linear motor stage, degradation of precision accuracy is commonly observed. The common used method for improving the accuracy is with laser interferometer to measure positioning errors, from which errors the corresponding error map can be built. The error map is then stored in motion controller to real-time compensate the positioning error. Since this method requires a reference position as the starting point of for error compensation with the pre-built error map, the reference position inevitably requires high repeatability so that the error map can effectively compensate the positioning error. Although reference signal generated by optical sensors has high repeatability and narrow pulse width, but it cannot maintain performance under severe ambient conditions caused by oil, water or dust. Hall-effect sensor can be used under severe ambient conditions; however, its signal has low repeatability and wide pulse width. It is then inappropriate for high precision requirements. This research presented in this paper is on the novel application of Wiegand effect for generating a reference signal. Wiegand effect can generate sharp pulse and the triggering of the pulse is independent of drive frequency. In this research, we use experiments and simulations to examine the relationship between different designs of magnetic circuit and repeatability of Wiegand pulse, which are later used to optimize the magnetic design of the system to improve the repeatability of Wiegand pulse.