He was charged with molesting seven girls, many of whom are gymnasts, while working for USA Gymnastics and Michigan State University.
As part of the plea deal, Nassar, 54, could face at least 25 years in prison.
The hearing comes after a third former US Olympian, Gabby Douglas, accused him of sexual abuse.
In a statement to the court on Wednesday, Nassar said he was pleading guilty to “move the community forward and stop the hurting”.
“I’m so sorry that this was like a match that turned into a forest fire, out of control,” he said.
“I want them to heal. I want this community to heal. I have no animosity toward any one. I just want healing. It’s time.”
“You used that position of trust that you had in the most vile way – to abuse children,” Ingham County Court Judge Rosemarie Aquilina said, noting that sex abuse is a nationwide “epidemic”.
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