Shortly after DeMotte's resignation in 1891, Joseph P. Naylor, head of the Indiana University physics department, was persuaded to come to DePauw as the new professor of physics. As the story goes, Naylor decided to accept DePauw's offer because he felt that "DePauw had a greater future...and a better [base]ball team." Indeed, at the time DePauw was the largest institution of higher learning in the state and had a relatively well-established physics program.

Naylor, a native of Pennsville, Ohio, had done some undergraduate work at Adrian College in Michigan before joining the work force as a watchmaker and draftsman. In 1881 he returned to academia to teach high school physics in Indianapolis and two years later entered Indiana University in pursuit of a graduate degree in physics. In 1885 he became among the first to receive an M.S. degree in physics from that institution; the following year, he was named professor of physics there.

The physics program taught by Naylor in his first year at DePauw consisted of six courses. Courses One and Two were the first and second semesters of the introductory physics course; lecture sessions met four times a week and an additional six hours per week were spent in the laboratory. Course Three, Theory of Electrical Measurements, was a staple of the curriculum for the next 70 years; laboratory investigations of magnetism, static electricity, and direct current circuits were the main order of business. Theory of the Dynamo/Electric Lighting and Photometry was the title of Course four, which in a few years became a more general Advanced Laboratory course. Finally, Courses five and six, Mathematical Physics, were a catch-all for various advanced treatments of vibratory motion, sound, electromagnetism, optics, and thermodynamics; the topics were varied each year to meet the needs of the students. In time, as department offerings became more diversified, many of the subject areas in Mathematical Physics were split off into separate courses.

In the 1890s, visitors to campus in search of the physics department would be directed to the building known as Middle College, a four-story structure that stood on the location presently occupied by Harrison Hall. On the first floor of Middle College were the physics lecture and reading rooms, an equipment room, a machine shop, and an area for the general laboratory; in the basement, a 15-horsepower engine chugged away, driving three dynamos that furnished current for the electrical experiments upstairs. The labs were outfitted with several fine instruments, including what was then one of the best spectrometer gratings (made by Henry Rowland of Johns Hopkins, with approximately 15,000 ruled lines per inch) in the United States.

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