Thomas Jonathan Burrill was named acting regent to succeed Peabody. Burrill graduated from Illinois State Normal University in 1865. He was an early professor of botany and horticulture during the nascent stages of development for these disciplines and was appointed vice president in 1882. Burrill was known nationally and abroad for his work in botany. His original research on the bacterial causes for plant and fruit disease led to the development of preventative treatment methods, the first major conceptual advance by an American in the developing field of plant pathology.
Burrill proved to be both a devoted teacher and wise administrator. He immediately addressed student unrest by lifting the ban on fraternities and declaring military drill no longer mandatory. He then made improvements for faculty including the reorganization of internal government, the creation of a tenure system and sabbatical leaves, and the establishment of salary classification scales. He asked legislators for a half-million dollars and received an unprecedented appropriation of nearly $300,000. Burrill then created a publicity committee with the goal of improving the statewide image of the University of Illinois.
The campus received much-needed physical improvements. Electric lights were installed in buildings, streets were paved, construction began on privately owned rooming houses, and the University colors of blue and orange were displayed. New buildings and programs included the Natural History Building, the Graduate School, the first summer school and the first Extension program. The entire bird collection from the Columbian Exposition of the 1893 Chicago World's Fair was housed in the Museum of Natural History located in the center of the Natural History Building.
At his retirement, Burrill had served the institution for nearly 50 years. He could have been appointed from acting regent to a permanent basis, but he preferred his work as teacher and scientist.