linguistic:paraphrasing, structural:reformatting, quality:correction
19th century

The trustees worked alongside four notable university presidents, Charles W. Eliot of Harvard University, Andrew D. White of Cornell University, Noah Porter of Yale College, and James B. Angell of University of Michigan. They each supported Daniel Coit Gilman to lead the new university and he became the university's first president. Gilman, a Yale -educated scholar, had been serving as president of the University of California, Berkeley prior to this appointment. In preparation for the university's founding, Gilman visited University of Freiburg and other German universities.

Gilman launched what many at the time considered an audacious and unprecedented academic experiment to merge teaching and research. He dismissed the idea that the two were mutually exclusive: "The best teachers are usually those who are free, competent and willing to make original researches in the library and the laboratory," he stated. To implement his plan, Gilman recruited internationally known researchers including the mathematician James Joseph Sylvester; the biologist H. Newell Martin; the physicist Henry A. Rowland, the first president of the American Physical Society, the classical scholars Basil Gildersleeve, and Charles D. Morris; the economist Richard T. Ely; and the chemist Ira Remsen, who became the second president of the university in 1901.

Gilman focused on the expansion of graduate education and support of faculty research. The new university fused advanced scholarship with such professional schools as medicine and engineering. Hopkins became the national trendsetter in doctoral programs and the host for numerous scholarly journals and associations. The Johns Hopkins University Press, founded in 1878, is the oldest American university press in continuous operation.

With the completion of Johns Hopkins Hospital in 1889 and the medical school in 1893, the university's research-focused mode of instruction soon began attracting world-renowned faculty members who would become major figures in the emerging field of academic medicine, including William Osler, William Halsted, Howard Kelly, and William Welch. Students came from all over the world to study at Johns Hopkins and returned to their sending country to serve their nation, including Dr Harry Chung (b. 1872) who served as a diplomat in the Manchu Dynasty and First Secretary to the United States. During this period Hopkins made more history by becoming the first medical school to admit women on an equal basis with men and to require a Bachelor's degree, based on the efforts of Mary E. Garrett, who had endowed the school at Gilman's request. The school of medicine was America's first coeducational, graduate-level medical school, and became a prototype for academic medicine that emphasized bedside learning, research projects, and laboratory training.

In his will and in his instructions to the trustees of the university and the hospital, Hopkins requested that both institutions be built upon the vast grounds of his Baltimore estate, Clifton. When Gilman assumed the presidency, he decided that it would be best to use the university's endowment for recruiting faculty and students, deciding to, as it has been paraphrased, "build men, not buildings." In his will Hopkins stipulated that none of his endowment should be used for construction; only interest on the principal could be used for this purpose. Unfortunately, stocks in The Baltimore and Ohio Railroad, which would have generated most of the interest, became virtually worthless soon after Hopkins's death. The university's first home was thus in Downtown Baltimore, delaying plans to site the university in Clifton.