Sir Alan Parker – who had been due to finish his 10-year term in December – said the “complex mix of challenges the organisation and the sector is facing” was the reason for his early departure.
He has also stepped down from the boards of the Save the Children Association.
During his time in the role, Save the Children UK was forced to deal with what Sir Alan referred to in his resignation letter as “unacceptable workplace behaviour, involving harassment, in our head office in Farringdon in 2012 and 2015”.
Three complaints of misconduct were made against Justin Forsyth, the former Save the Children CEO, and Brendan Cox, the husband of murdered MP Jo Cox.
A leaked report from 2015 suggested that Mr Parker’s “very close” relationship with Mr Forsyth may have affected how allegations were handled.
Mr Forsyth left the charity in 2016, having previously apologised unreservedly to the three women who made complaints. He quit as UNICEF’s deputy executive director earlier this year.
Mr Cox, who was Save the Children’s chief strategist, admitted he had “made mistakes” which caused some women “hurt and offence”. He had quit in 2015 amid the allegations, but denied it was why he left.
He also quit two charities he set up in memory of his wife when the allegations were published earlier this year.
The Charity Commission is now reviewing Save the Children’s handling of both cases.
The leader of the Woman’s Equality Party, Sophie Walker, welcomed Sir Alan’s departure, but said the problems in the charity and NGO sector went beyond any one individual.
A former Save the Children employee who stormed a board meeting in March to protest the handling of harassment cases said: “Save the Children need to be accountable for their culture of secrecy and the abuses of power which harmed so many staff, including men.”
Alexia Pepper de Caires, who is also the co-leader of the Women’s Equality Party Hackney branch, added: “Today is a huge step for Save the Children and other charities so that they wise up, acknowledge previous failings and start real reform.”
The Oxfam scandal earlier this year, which has rippled out to other aid organisations including Save the Children, has led to a surge in reported cases of charity beneficiaries and staff being put at risk of harm.
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UNICEF chief Justin Forsyth resigns after ‘inappropriate behaviour’
Ex-Save the Children boss apologises for ‘inappropriate’ behaviour with female colleagues
The Charity Commission has opened 440 new cases – some involving “potentially criminal” allegations – after receiving 523 fresh reports in February and March.
A Charity Commission report will be published into the key findings once the review is completed