The Charity Commission said it was “in regulatory engagement” with The Save The Children Fund in 2015-16, after the charity reported a serious incident relating to allegations of misconduct and harassment against a senior staff member.
The regulator also received an anonymous complaint about the charity’s response to further allegations against senior staff members.
Michelle Russell, of the Charity Commission, said: “This inquiry centres specifically on how the charity handled complaints in 2012 and 2015 about senior members of staff, and how the charity responded to and managed public and media scrutiny of those events in 2018.
"Opening a formal investigation does not necessarily mean that we have concluded that there has been wrongdoing by the trustees of The Save the Children Fund.
"However, we do have questions that must be answered.”
It was reported in February that Save the Children had apologised to female employees who complained of inappropriate behaviour by former chief executive Justin Forsyth.
This came after Brendan Cox, the widower of murdered MP Jo Cox, admitted that he had made “mistakes” and behaved in a way that caused some women “hurt and offence” when he was working at the charity in 2015.
Among other issues, the new inquiry will examine whether trustees made decisions about the public relations handling of the historic allegations "appropriately" and whether they disclosed "fully, frankly and accurately" serious incidents relating to staffing matters to the Commission.
It comes after a commission on loneliness set up by Mrs Cox was wound up.The work will be continued through a parliamentary group led by Mrs Cox’s friend Rachel Reeves MP.