Despite calls for improved data-collection efforts tracking transgender and gender nonconforming (TGNC) people in science, technology, engineering, and mathematics (STEM) education, there have been no reports of TGNC continuation in STEM majors at the university level. Using national, longitudinal data from the Higher Education Research Institute at the University of California, Los Angeles, we analyzed the experiences of 20,910 students who indicated an initial intent to major in a STEM field and found that TGNC students (n = 117) continue in STEM majors at a rate ~10% lower than their cisgender peers. This gap persists despite TGNC students' high levels of academic ability and academic self-confidence. Through multilevel regression modeling, we found this difference is not explained by experiences that have predicted the likelihood of cisgender students leaving STEM. The only significant predictor of STEM attrition for TGNC students in our model was whether they sought personal counseling; TGNC students who more frequently sought personal counseling were 21% less likely to remain in STEM majors. Overall, TGNC students leave STEM at rates similar to or higher than other minoritized groups, building the case for a multifaced, intersectional approach to addressing diversity and equity in the preparation of the future STEM workforce.