Her resignation follows a review of the women's basketball program that put her, as well as her three assistants, on paid administrative leave.
Hatchell had been coaching at Carolina for 33 years.
Additionally, Hatchell, a 2013 Hall of Fame inductee, is the winningest women's basketball coach in Atlantic Coast Conference history. She has a career record of 1,023-405 and is 751-325 mark in 33 years at UNC with a national title in 1994.
Cunningham also said in the statement that the school will now begin searching for a new head coach for the program.
School spokesman Steve Kirschner said April 1 in a statement that the review was "due to issues raised by student-athletes and others." He did not specify what those issues were.
The entire women's basketball coaching staff was suspended while the review took place, UNC-Chapel Hill said.
"The University of North Carolina is committed to the well-being of our student-athletes and to ensuring that they have the best experience possible in and outside of competition. Due to issues raised by student-athletes and others, the University has initiated a review of our women's basketball program," the university said in a statement.
A firm interviewed 28 people and said there were complaints of "racially insensitive comments" and those concerns were not handled in a "timely or appropriate manner."
The firm also said "players and medical staff expressed frustration" that there was "pressure to play" and players were put back on the court "before they were medically ready."
"I would not expect that. I don't know what happened," said UNC student Smith Carpenter.
Another student said she was caught off-guard by the news.
"I'm honestly kind of surprised," said student Oheneba Boateng. "She's been coaching here for a while and since this whole story has come up, not a lot has been said about it on campus."
When ABC11 called the Athletic Department and tried to substantiate the claims, an official would not comment.