Perry's departure deals another blow to the embattled governing body, as it struggles to rebuild its reputation following the Larry Nassar sexual abuse scandal.
Nasser was jailed for life in January for abusing more than 250 athletes.
Senior coach Mary Lee Tracy was ousted just three days after her appointment last Tuesday.
Tracy came under fire from Nassar's victims over comments she made in late 2016 -- when the first allegations of abuse against Nassar had already begun to emerge -- in which she described the doctor as "amazing."
Survivors said Tracy had supported Nassar and they wanted her gone.
So she has left, taking Perry with her in the process.
"USA Gymnastics has appointed someone who, in my view, supported Nassar, victim-shamed survivors, & has shown no willingness to learn from the past," Olympic gold medallist Aly Raisman, who was among Nassar's victims, tweeted.
The fiasco of Tracy’s appointment to a senior coaching role and departure within a few days angered the United States Olympic Committee, which on Friday warned that changes to USA Gymnastics's leadership were inevitable.
USA Gymnastics chairwoman Karen Golz said Tuesday Perry had led the organisation "under very difficult circumstances."
However, she said the sport's body was on the road to recovery.
"In the wake of horrific events that have impacted our athletes and the entire gymnastics community, USA Gymnastics has made progress in stabilising itself and setting a new path to ensure that the safety and interests of our athletes remains at the heart of our mission," Golz said.