During this early period of his career Dr. Pepper labored with untiring zeal in the practice of his profession, and he also became eminently successful as a teacher. In 1877 he set forth his views on higher medical education in an address at the opening of the one hundred and twelfth course of lectures in the University Medical School.[45] At that time a very low standard existed in the medical schools of our country, and Dr. Pepper, in his address, urged the following reforms:

1. The establishment of a preparatory examination.

2. The lengthening of the course to at least three full years.

3. The careful grading of the course.

4. The introduction of ample practical instruction of each student both at the bedside and in laboratories.

5. The establishment of fixed salaries for the professors, so that they may no longer have any pecuniary interest in the size of their classes.

It was a source of gratification to Dr. Pepper that he lived to see all these reforms in medical education adopted. On the extension of the medical course to four years he subscribed $50,000 toward a permanent endowment of $250,000. As early as 1871 he began to urge the establishment of a university hospital, the subject being first discussed in a conversation with Dr. H. C. Wood and Dr. William F. Norris. An appeal was made to the public, and Dr. Pepper was made chairman of a finance committee. By May, 1872, a splendid site and $350,000 for building and endowment had been secured. Dr. Pepper was selected as chairman of the building committee, and work on the hospital was pushed so rapidly that it was ready for patients on July 15, 1874.

When Dr. Charles J. Stillé resigned the provostship of the university in 1881, Dr. Pepper was elected as his successor. The executive abilities which he had displayed in connection with the founding of the new hospital made him the natural choice of the trustees. Although his private practice had increased to immense proportions, besides being occupied with his duties as a clinical professor, Dr. Pepper accepted the provostship. To the duties of this office he devoted the best years of his life. The extent of his practice and the demands made upon his time by the university would have appalled an ordinary man, but his capacity for labor appeared to be without limit, his working day often exceeding eighteen hours. His administration was characterized by the unification of the various schools of the university, besides the founding and equipment of several new departments. In one of his annual reports Dr. Pepper defined the broad policy of the university in the following appropriate language: "The university is truly the voluntary association of all persons and of all agencies who wish to unite in work for the elevation of society by the pursuit and diffusion of truth."[46] In other words, Dr. Pepper regarded the functions of the university as not simply an institution of instruction, but also of research. To this end every effort was made to open up new fields of investigation and to widen the scope of the university. During his provostship thirteen new buildings were erected, and the following departments, or schools, were organized:

1.The Department of Finance and Economy.
2.The Department of Philosophy.
3.The Department of Veterinary Medicine.
4.The Department of Biology.
5.The Department of Physical Education.
6.The Department of Archæology and Paleontology.
7.The Department of Hygiene.
8.The Graduate Department for Women.
9.The School of Architecture.
10.The School for Nurses in the University Hospital.
11.The Veterinary Hospital.
12.The Wistar Institute of Anatomy and Biology.

Dr. Pepper took particular interest in the Department of Archæology and Paleontology connected with the university. For a number of years he was president of its board of trustees, while it was largely through his efforts that the Babylonian Exploration Fund was formed.[47] It was Dr. Pepper's ambition to have at the university well-equipped laboratories that would offer an opportunity for original investigation in medical science. The establishment of the Laboratory of Hygiene, in 1892, was the first step in this direction, soon to be followed by Dr. Pepper's gift of the Laboratory of Clinical Medicine. This laboratory was founded in memory of his father, the late Dr. William Pepper. The gift is unique in that it is made for the purpose of promoting and stimulating original research, and improving the methods of diagnosing and treating the diseases of human beings. Another field of work in the laboratory is that of giving advanced and special instruction to men who have already obtained the degree of Doctor of Medicine. At the opening of the laboratory in 1895 Dr. William H. Welch, of Johns Hopkins University, said, "To the small number of existing clinical laboratories the William Pepper Laboratory of Clinical Medicine is a most notable addition, being the first laboratory of the kind in this country, and it is not surpassed by any in foreign countries."[48]