Sullivan's notice to the court is due to be made public Monday.
The lawyer and his wife, Stephanie Robinson, who also works at the school, will not be renewed as deans at Harvard's Winthrop House once their terms expire next month.
Sullivan's decision has no impact on Jose Baez, the noted criminal lawyer now leading Weinstein's defense, or the rest of the team. Sullivan is a noted expert on criminal law and criminal procedure and is director of the Harvard Criminal Justice Institute.
Weinstein spokesman Juda Engelmayer told ABC News Saturday evening that Weinstein "is extremely grateful to Ronald Sullivan for his work with him until now, and for Ron's offer to advise where he can going forward."
"Mr. Sullivan believed that Mr. Weinstein deserved a vigorous defense, and it is a sad moment for us all right now," Engelmayer said. "We, as a country, have now reached the point when a Harvard lawyer and professor cannot serve his duty to, and belief in, the law and defend a person who may be deemed unpopular or unworthy of a legal defense by segments of the public."
The Harvard Crimson, the college's newspaper, was the first to report on Sullivan's exit.
The Harvard Black Law Students Association supported Sullivan's decision to represent Weinstein, saying in a statement released March 31, "HBLSA finds it important that we speak to the controversy and make the ask of Harvard University to both unequivocally support survivors of sexual violence and to do so in a way that does not scapegoat Professor Sullivan for the University’s failings to address sexual violence on campus."
Weinstein is due to go on trial in September on charges of rape and sexual assault. He was arrested nearly a year ago and is out on bail.
He is set to go on trial on accusations made by two women in New York, but has been accused of improper conduct by dozens of other women over decades.
Weinstein, 66, has been investigated by the New York City Police Department, the Manhattan District Attorney’s Office, the New York Attorney General’s Office, the Los Angeles Police Department and U.K. authorities.
He has denied all allegations of nonconsensual sex.
Editor's note: A former version of this story stated that The New York Times was the first to report on Sullivan's exit from Harvard University. The story has been updated to reflect that The Harvard Crimson was the first to report that information.