Katie Meyler, the CEO of charity More Than Me, announced she would step aside after a report by ProPublica and Time magazine revealed the abuse.
More Than Me says they have taken steps to safeguard girls at the school, which is devoted to women's empowerment.
The group has also created a panel to review the investigation.
The non-governmental organisation's (NGO) advisory board recommended an independent investigation into allegations of widespread abuse and negligence at the institution, which exists to protect young Liberian girls from sexual abuse and exploitation.
In a statement on Monday, a committee of seven Liberian government agencies said it met twice since the story was published on Thursday, with the aim "to taking the appropriate legal actions to protect the children and ensure they are safe", Time magazine reported.
The NGO had received almost $600,000 (£456,000) from the US government, and Ms Meyler had been praised by celebrity philanthropists including Oprah Winfrey, Bill Gates and Warren Buffett. She had also received an invitation to the White House by former President Barack Obama.
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