Dr. Pepper realized more and more every year that the vast extent of the university interests demanded the undivided activity of its head. In 1894 he resigned the office of provost, stating at the time that, as it became necessary for him to choose between administration work and medical science, his devotion to the latter determined his choice. His administration was an eventful one, during which the university evolved from a group of disconnected schools to a great academic body. In 1881 its property in land amounted to fifteen acres, while in 1894 it controlled fifty-two acres in a continuous tract. In 1881 the university property was valued at $1,600,000; in 1894 it exceeded $5,000,000. The teaching force in 1881 numbered 88 and the students in all departments 981; in 1894 the former were 268, and the attendance had reached 2,180, representing every State in the Union, as well as thirty-eight foreign countries.
Dr. Pepper became well known as an author on medical subjects. He founded the Philadelphia Medical Times, and was its editor for two years. In 1885 he edited a System of Medicine by American Authors, a work that has been considered a leading authority on medical subjects. He also edited a book of medical practice by American authors, and, with Dr. J. F. Meigs, issued a work on Diseases of Children. He was Medical Director of the Centennial Exposition in 1876, and for his services he received from the King of Sweden the decoration of Knight Commander of the Order of St. Olaf.
Dr. Pepper showed an unbounded interest in behalf of any movement that would benefit the community in general. He was one of the first to realize the advantage that would accrue to Philadelphia should she become a museum center. The Philadelphia Commercial Museum was established in October, 1893, with Dr. Pepper as president of the board of trustees. The old offices of the Pennsylvania Railroad Company were leased, and exhibits were secured from the Latin-American countries, Africa, Australia, Japan, and India, forming the largest permanent collection of raw products in existence. Referring to the great value of the museum, Dr. Pepper spoke as follows in his address of welcome at the first annual meeting of the advisory board:
"It would seem clear, however, that no method of studying industries and commerce can be scientific and complete which does not include the museum idea as now comprehended. The museum aims to teach by object lesson the story of the world, past and present. The Biological Museum presents the objects of human and comparative anatomy, arranged scientifically and labeled so fully as to constitute the best text-book for the study of those subjects. The Museum of Natural History does the same in its field. The Museum of Archæology shows the progress of the race from the most archaic times, the different types of human beings, their mode of living, their forms of worship, their games, their weapons, their implements, the natural products which they used for subsistence, in their industries, and in their arts, the objects of manufacture or of art which they produced, and the manner in which they disposed of their dead.
"The natural products and manufactured articles, which constitute the material of commerce, come necessarily into such a scheme, and the long-looked-for opportunity of establishing a commercial museum upon a truly scientific basis presented itself when, at the close of the Columbian Exposition at Chicago, it was possible, through the enlightened liberality of the municipal authorities of Philadelphia and the invaluable services of Prof. W. P. Wilson, to secure vast collections of commercial material, which was so liberally donated to the Philadelphia museums by nearly all the foreign countries of the globe."
It was Dr. Pepper's idea to have the University Museum and the Commercial Museum situated near each other, on the plan of the South Kensington Museum. To this end the City Councils, in 1896, passed an ordinance giving over to the trustees of the Commercial Museum sixteen acres of land for the erection of suitable buildings. When all the plans are carried out the city will have unrivaled facilities for the study of civilization, past and present.
One of the most enduring monuments to Dr. Pepper's zeal and generosity is the Free Library of Philadelphia. In 1889 his uncle, George S. Pepper, bequeathed the sum of one hundred and fifty thousand dollars "to the trustees of such Free Library which may be established in the city of Philadelphia." From the beginning Dr. Pepper took a warm interest in the Free Library movement. It was under his leadership that the library was organized, and he was made the first president of its board of trustees. Speaking of his activity in this direction, the librarian, Mr. John Thomson, said: "No detail was too small for his personal attention. No plan for its future growth was too large for his ambitious hope of both public and private support. The remarkable and rapid increase in the circulation of the Free Library, the multiplication of its branches, the organization of all its departments on a broad and generous plan, his success in enlisting a large number of able fellow-workers, his clear, plain statements to Councils and the city authorities, his activity in securing needed legislation at Harrisburg, were some of the results of that intelligent energy which enabled him to do so much and to do it so well." The bequest of the Pepper family has been supplemented by ample appropriations by the City Councils, and the Free Library is now one of the most important institutions in Philadelphia. The library at present has twelve flourishing branches, while the combined circulation of the system for the year 1898 was 1,738,950 volumes.
Dr. Pepper was also connected with many scientific bodies. He was Vice-President of the American Philosophical Society, and President of the first Pan-American Medical Congress in 1893. He was a Fellow of the College of Physicians; President of the Philadelphia Pathological Society from 1873 to 1876; Director of the Biological Section, Academy of Natural Sciences; President, in 1886, of the American Climatological Association; President of the Foulke and Long Institute for Orphan Girls; President of the First Sanitary Convention of Pennsylvania; and in 1882 he was a member of the Assay Commission of the United States Mint. He received the degree of LL. D. from Lafayette College in 1881, and from the University of Pennsylvania in 1893.
In 1873 Dr. Pepper married Miss Frances Sargeant Perry, a lineal descendant of Benjamin Franklin, and a granddaughter of Commodore Oliver Hazard Perry. Four sons were born, of whom three survive—Dr. William Pepper, Jr., Benjamin Franklin Pepper, and Oliver Hazard Perry Pepper. Failing in health, Dr. Pepper went to California early in the summer of 1898, where he died of heart disease on July 28th of that year. His body reached Philadelphia on August 6th. Funeral services were held in St. James's Protestant Episcopal Church, after which the body was cremated, and the ashes interred in Laurel Hill Cemetery. The American Anthropometric Society received, by the conditions of his will, Dr. Pepper's brain. Among the members of this society were Dr. Joseph Leidy, Phillips Brooks, and Prof. E. D. Cope. The articles of membership of the Anthropometric Society require that each member contribute his brain in the interests of science.
Dr. Pepper's death was followed by many expressions of sorrow from learned societies in various parts of the world. One of the most beautiful tributes was the memorial meeting held in the city of Mexico on September 12th. The leading medical and scientific societies of Mexico assembled in the hall of Congress to do honor to the work and character of Dr. Pepper. President Diaz occupied the chair, and about him were gathered the leading citizens, officials, and scientists of Mexico. Representatives of the National Medical School and the Board of Health eulogized Dr. Pepper, while Hon. Matias Romero spoke of him not as a physician, but as an "altruist who had consecrated himself to doing good for his fellow-men."