Faculty advisors play an important role in the development of graduate students. One group for which the advising relationship has been shown to be especially crucial is women in science, technology, engineering, and mathematics (STEM). We designed two studies to assess the advising alliance for women in STEM graduate programs using the student version of the Advisor Working Alliance Inventory (AWAI) along with additional content developed by our team. Study 1 (N = 76) was developed to assess item performance and the initial structure with a pilot sample of undergraduate and graduate students in science and engineering. Study 2 (N = 293) was designed to assess the advising alliance exclusively for women in STEM graduate programs. Our results indicated that an alternative alliance structure may exist for women in STEM and in Study 2 two factors emerged, which indicated that instrumental support and psychosocial support are two salient factors for women in STEM.