Despite broad consensus that high-skilled immigration can contribute to innovation and economic growth (1–3), there is considerable controversy regarding how to reform immigration policies, including for workers in science, technology, engineering, and mathematics (STEM) professions. Much attention has centered on entry-level IT workers (4, 5), but less consideration has been given to the visa pathways of STEM doctorates (6, 7) who, unlike entry-level IT workers, can bring firms advanced training at the frontiers of science and technology and contribute disproportionately to innovation and entrepreneurship relative to workers with bachelor’s or master’s degrees (3). We provide new insights on the visa progression, qualifications, and starting salaries of STEM doctorates in the U.S. context from a survey that follows a cohort of 1597 U.S. citizen (69.7%) and foreign-born (30.3%) science and engineering Ph.D.’s from U.S. research universities into their first-time industry R&D employment [see details in the supplementary materials (SM)]. We show that the H-1B visa has become the predominant first step for STEM Ph.D.’s employed in industrial R&D, not because it is legally required or the most suitable visa but because of inefficiencies and delays on the path to permanent residency. Our findings show that the H-1B—a highly contentious visa used primarily for entry-level workers—may be an inefficient pathway for U.S.-trained STEM doctorates and suggest the need to rethink visa policies to retain these highly specialized workers.