During her fourth year of medical school, Sabin announced to some classmates that she planned to pursue laboratory medicine and teaching rather than medical practice. Her 1900-1901 internship at Johns Hopkins Hospital did not change that decision. However, the university trustees refused to hire a woman to the medical school faculty. Faculty, they believed, should be eminent physicians of established reputation or the most promising young researchers. Women physicians were rarely acknowledged as either, regardless of their credentials. Sabin used her fellowship from the Baltimore Association for the Promotion of University Education for Women to continue working in Mall's laboratory during 1901-1902. The work she did on the lymphatic system that year was so outstanding and received so much praise from her colleagues that the trustees made an exception to their usual policies: Sabin was hired as an assistant instructor in the Anatomy Department in 1902, promoted to associate instructor in 1903, and to associate professor in 1905.
During her many years in the Anatomy Department, Sabin taught anatomy, embryology, and histology to nursing and medical students, and supervised budding researchers. She became a legendary teacher, not just for her intellectual rigor, but for her warmth and her willingness to engage her students on many levels. She worked side by side with them in the labs but also invited them to dinner parties at her home. Many students became lifelong friends and colleagues. Speaking at Sabin's 80th birthday celebration, one former student recalled that Sabin's teaching inculcated a love of scholarship, a high regard for learning, a fostering of the spirit of inquiry and of intellectual curiosity; he praised "her emphasis upon the duty and pleasure of extending rather than merely acquiring knowledge, her impatience with inaccuracy and with stupidity, her unswerving loyalty to the highest ideals of natural science."
Sabin also continued her investigation into the origins of the lymphatic system during her first fifteen years at Hopkins, and published steadily, building her reputation for meticulous and innovative research. Anatomists and embryologists had mapped much of the human body by 1900, but the origins of some tissues and systems were still poorly understood. How were the smallest lymphatic channels formed? Were they open, perhaps connecting to the capillaries, or closed? Sabin, using less-developed pig embryos rather than the nearly mature ones used by earlier investigators, and injecting the lymph vessels with colored material, found that they arose as buds from the vein endothelium (tissue lining the vein), and grew outward as continuous channels by further budding. By making serial cross-sections of injected and non-injected embryos, she was also able to show that the ends of the lymphatic channels were closed and that they did not open into the spaces between tissues, or derive from those spaces. These observations were the opposite of what other anatomists had predicted and generated some controversy.
After 1917, her work on lymphatics led Sabin to study the growth of blood vessels and how blood cells are generated by the vessels' endothelium in embryos. For this research she used living tissue, watching cellular growth in "hanging drop" preparations of chick embryos. She was able to see red blood cells coming from the blood vessels' endothelium on the second day of incubation, and white cells on the third day. During these years, Sabin made several trips to Europe, and visited labs in Leipzig and other German research centers to learn more about tissue culture and staining of living tissues. She was then able to perfect several techniques for "supravital" staining, which allowed differentiation of cell types, especially immune systems components, such as the monocytes, a type of white blood cell.
In June 1917, after twelve years as an associate professor, Sabin was promoted to full professor in the Department of Anatomy. Five months later, Franklin Mall died, leaving the department's chair vacant. As Mall's protégée and a longtime member of the faculty with an excellent research and teaching record, Sabin seemed a natural choice to succeed him as chair. To the surprise of many, she was not among those considered for the position, and it was given to Lewis Weed, one of her former students. Her students were outraged and petitioned to have the matter reconsidered, and the Baltimore Association for the Promotion of University Education for Women complained vigorously to the university administration. Sabin herself accepted the disappointing decision without protest. Asked if she would stay at the Hopkins following such unfair treatment, she replied, "Of course I'll stay. I have research in progress." She remained at Johns Hopkins until 1925.
Even if the Johns Hopkins administration had declined to acknowledge Sabin's abilities in a concrete way, the rest of the world did not. In 1921, the Rockefeller Foundation invited her to speak at the opening of its Peking Union Medical College and she traveled to China to participate in the ceremonies. In 1924, the American Association of Anatomists elected her as their first woman president. And the following year Sabin became the first woman elected to membership in the National Academy of Sciences.