Ex-Save the Children chief executive Justin Forsyth has resigned from Unicef as he says he does not want coverage of his past to "damage" the charities.
Mr Forsyth faced three complaints of inappropriate behaviour towards female staff before leaving Save the Children, the BBC reported this week.
He was accused of sending inappropriate texts and commenting on what young female staff were wearing.
He said he "apologised unreservedly" to the three workers at the time.
Mr Forsyth said the reason for his resignation as Unicef's deputy director was not because of what he described as the mistakes he made in his former role at Save the Children.
"They were dealt with through a proper process many years ago," he said in a statement.
"There is no doubt in my mind that some of the coverage around me is not just to (rightly) hold me to account, but also to attempt to do serious damage to our cause and the case for aid."
A statement from Unicef said it was grateful to Mr Forsyth for his work over the past two years.
An investigation by BBC Radio 4's PM programme found that the complaints against Mr Forsyth included women receiving a series of inappropriate texts and comments on how they looked, what they were wearing and how he felt about them.
If they did not respond, Mr Forsyth would follow up his messages with an email, asking if they had seen the text.
If they still did not respond, he would ask someone to send them to him for a "quick word".
Save the Children said it had commissioned "a root and branch review of the organisational culture" at the charity "addressing any behavioural challenges among senior leadership".
The charity said concerns were raised about "inappropriate behaviour and comments" by Mr Forsyth in 2015.
It said two trustees carried out separate investigations into a total of three complaints made by female employees.
"Both reviews resulted in unreserved apologies from the CEO. All the parties agreed to this and the former CEO apologised to the women in question. At that time the matters were closed."
Speaking earlier this week, a spokesman for Unicef said the charity had not been aware of any of the complaints against Mr Forsyth at the time of his recruitment in 2016.
"There have been no such complaints concerning Mr Forsyth at Unicef," he added.
The allegations come after Brendan Cox - the husband of murdered MP Jo Cox - quit two charities he set up in memory of his wife amid allegations of inappropriate behaviour.
The Charity Commission said it had "extensive regulatory engagement" with Save the Children after allegations of misconduct and inappropriate behaviour were made against Mr Cox and Mr Forsyth between 2015 and 2016.