In 1895 he left MIT to become the fourth president of Lehigh University. Lehighs endowment was predominantly in the stock of the major company of its founder, Asa Packers Lehigh Valley Railroad. The Panic of 1893 crashed the market, brought the country into depression that lasted years, and nearly brought the university to financial insolvency. Many prominent railroads such as the Northern Pacific Railway, the Union Pacific Railroad and the Atchison, Topeka & Santa Fe Railroad went into bankruptcy, and over 15,000 companies and 500 banks failed. In order to gain new sources of funding, President Drown broke the university's ties with the Episcopal Church in 1897, qualifying the university for aid from the Commonwealth of Pennsylvania.  During his term, which started during a major financial crisis, he was able to save Lehigh from bankruptcy, grow enrollment, which had dipped seriously, grow academics, and even have one major building erected.
A broad intellectual with interests in various fields, he nonetheless thought the key to Lehighs success would be the school of technology.  There he sought to broaden and deepen the offerings, increase the quality and quantity of laboratory space, equipment and apparatus, as funding permitted.  Additionally, and in consultation with the faculty and the board of trustees, he created many new tiers of teaching, including the associate and assistant professorships.  His idea was that this would create resources for top professors to be invited to Lehigh, and so help enlarge the curricula.  During his tenure, the universitys first emeritus professorship was granted (Harding of Physics), and first doctorate awarded (Joseph W. Richards).  Many new degrees in the technical school were now being offered, such as Metallurgy (1891), Electrometallurgy, and Chemical Engineering (1902).  The curriculum leading to a degree in arts and engineering was established, as was the department of zoology and biology.  New courses (majors, that is, or degree offerings, as it is now known) were also adopted in geology, and physics.
Dr. Drown eventually gained in popularity on campus, with his forward ideas, success, idiosyncratic pince-nez glasses and mustache.  Faculty members eventually came to refer to Dr. Drown as "chief".  Unfortunately, T. M. Drown would not live long enough to see all his ideas to fruition, as he died in office, following abdominal surgery, November 16, 1904, effectively ending his term.
Williams Hall (1903), a Beaux Arts inspired Brick structure, was erected to house the growing departments of Biology and Geology, among other functions.
In 1908, Lehigh University opened up Drown Hall which now houses Lehigh's English Department.