Now Murphy has abandoned the office furniture, which he said he forgot had a plaque on the front that said "Woodrow Wilson's Desk."
"As soon as I was able to get a replacement, which was not as easy as I thought, I got one and I think it was the right thing to do," Murphy said during a press conference on Monday.
The country is having a "reckoning," Murphy said, and "Woodrow Wilson and his legacy are being dragged along as they should be."
Wilson, who was the country's 28th president from 1913 to 1921, once called racial segregation a "benefit" and said slaves "were happy and well cared for."
When he served as president of Princeton University between 1902 and 1910, he denied the admission of African American men and tried to exclude them from the history of the school.
Murphy's decision to change his desk comes after Princeton removed Wilson's name from his school of public policy and a residential university.
"Wilson's racism was significant and consistent even by the standards of his time," Princeton President Christopher Eisgruber said in a statement last weekend.
"He segregated the federal civil service after it had been racially integrated for decades, thus leading the United States backward in its quest for justice. He not only agreed but joined the persistent practice of racism in this country, a practice that continues to hurt today. "
Monmouth University of New Jersey has also said it will remove Wilson's name from the Great Hall on campus. Instead, he will seek to honor its chief designer, Julian Abele, who was one of the first professionally trained African American architects.
CNN's Kristina Sgueglia, Jay Croft, Sheena Jones and Karen Smith contributed to this report.