Perry was hired around the time former national team doctor Larry Nassar pleaded guilty to sexually abusing more than 100 gymnasts, including Olympic gold medallists Aly Raisman and Jordyn Wieber.
The full board of USA Gymnastics, the sport's national governing body, resigned early this year after revelations that officials there had turned a blind eye to the accusations.
"In the wake of horrific events that have impacted our athletes and the entire gymnastics community, USA Gymnastics has made progress in stabilizing itself," Karen Golz, chair of the USA Gymnastics Board, said in a statement.
Golz thanked Perry "for her leadership under very difficult circumstances."
The Orange County Register, which reported the departure hours before USA Gymnastics announced it, said she was forced out amid pressure from the U.S. Olympic Committee, according to two unidentified people it said were familiar with the process.
Perry did not immediately respond to a message seeking comment, and USA Gymnastics spokeswoman Leslie King declined to comment on the report. The group's statement did not say why she was leaving.
Perry had been criticized for not reaching out to the victims of Nassar's sexual abuse and for focussing on marketing rather than structural changes, the Register said.
In addition, USOC CEO Sarah Hirshland said on Friday night that it was "time to consider making adjustments in the leadership," USA TODAY reported.
In June, USOC acting CEO Susanne Lyons told reporters that Perry had "made a lot of good first steps but there is quite a long way to go.”
Nassar, who also was a doctor for athletes at Michigan State University, was convicted last year of sexually molesting gymnasts in incidents dating as far back as the 1990s and was sentenced in January to an effective life term in prison.
The sentencing followed an extraordinary weeklong hearing that saw a parade of Nassar victims tell their stories in raw and unflinching terms.
(Reporting by Peter Szekely in New York; Editing by Bill Trott and Tom Brown)
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