Throop served a year as interim chancellor before being named chancellor in 1928. Under his leadership, Givens Hall for the School of Architecture was built, the University's Extension Division became University College, and an affiliation with the Central Institute for the Deaf was begun. The medical school opened the Oscar Johnson Institute, the McMillan Hospital Clinics, and the Mallinckrodt Institute of Radiology.
Throop, although not without his critics on both campuses and admittedly not as gifted an administrator as some of his predecessors, nevertheless guided the University through tough financial times and declining enrollment spurred by the Great Depression and the looming Second World War, adopting pay cuts and establishing an Alumni Endowment Drive, a massive recruitment drive, and an endowment drive funded by local businesses. Still, the pressures of the times made these efforts less successful than they might have otherwise been. The tireless Throop once described his dedication and work ethic by saying, "The first element of success is work, the second is work, and the third is work."
He resigned the chancellorship in 1944 and died five years later.