Burton cut ties to the football program and most of the university, including transferring football scholarship money to students at the university's business school.
"After this slap in the face and embarrassment to my family, we are so upset that we are out of UConn," Burton wrote. "What this means is that we do not want to deal with people like you and your committee, whom we do not trust and cannot count on to make the correct decisions or do anything right with our money."
He said he will halt plans for the business school to train managers at his three companies in Connecticut.
Calls to Burton were not immediately returned.
Burton also blamed Hathaway for the decision of former UConn head football coach Randy Edsall to join the University of Maryland's football program earlier this month.
"When the press contacts me, I plan to tell them the truth and the entire story about how your lack of support was the primary reason Randy departed from UConn and how you did not even give the football team's largest donor the opportunity to provide any input about the head coaching job," Burton wrote.
Stacy Palmer, editor of The Chronicle of Philanthropy, said this is not the first time donors have asked for money back from charities. But it is rare, and she does not recall a past event in which the request was granted.
"Once donor the gives a check to a charitable institution and it's processed, you usually can't get it back," Palmer said. "What this is about is public relations. The resolution that they want to come to is to make other donors comfortable in giving to institution."