Mankaymer's resignation comes two weeks after she was asked to step down over her role in an ethics dispute involving Lloyd Ward, the group's chief executive officer.
Mankaymer was instrumental in opting for New York as the US candidate to bid for the 2012 Olympics and the USOC's recent internal conflict will not have escaped the International Olympic Committee's notice when it comes to looking at the potential bidding cities.
Seven USOC officers called for Mankamyer's resignation on January 21, saying she tried to interfere with the organization's investigation of Ward.
The case involved business negotiations between this year's Pan American Games in Santo Domingo and a Detroit-based energy company connected to Ward's brother. Ward wasn't punished after a finding that the discussions suggested a conflict of interest.
Stated Mankaymer: "This is a time when the USOC needs to refocus on its priorities and avoid public displays of disagreement. Because there appeared to be no possibility for peace unless I stepped aside, and with the thought that my action could make a positive difference for an organization which I have devoted almost 20 years, I have decided to resign."
Mankamyer's term of office was due to run through until 2004.
US Olympic Committee president Marty Mankamyer has resigned from her post, placing huge doubts over both the governing body and the validity of New York's bid to host the 2012 Olympics.
