This is the fifth public allegation of sexual assault against Murray.
Earlier, Murray had dropped his reelection bid in May amid four allegations of sexual abuse by four men who said that the mayor had sexually abused them years earlier, when they were teenagers.
One of the men had also filed a lawsuit against Murray in April alleging that the latter "repeatedly criminally raped and molested" him when he was 15 years old, in the 1980s.
Although Murray has denied all the allegations, he has decided to resign, which will take effect from Wednesday evening.
"While the allegations against me are not true, it is important that my personal issues do not affect the ability of our City government to conduct the public's business," he said in a written statement.
"To the people of this special city and to my dedicated staff, I am sorry for this painful situation," the statement further said. (ANI)