Annetts joined the charity in August after six years as chief executive of Dignity in Dying, which campaigns for patient choice for terminally ill people (Third Sector Online, 14 August).
She is believed to have disagreed with YWCA trustees over the future direction of the charity for disadvantaged young women and will not see out her notice period. Last month, Annetts interviewed senior managers in an attempt to establish the future direction of the organisation and improve its operations (Third Sector, 17 October).
Third Sector has learnt that there have been allegations of bullying within YWCA's senior management team. The charity has also faced questions over the use of £280,000 of charity funds, which were paid to HR consultancy Oasis School of Human Relations, with which it had a seven-year partnership.
In an internal YWCA newsletter published at the end of September, Annetts wrote that although the senior management team "appreciated the work Oasis had done on change management", the relationship had reached a natural end.
She also wrote about reducing bureaucracy, increasing the effectiveness of the organisation and making the charity more enterprising and confident.
The charity declined to discuss any specific allegations. A spokeswoman said trustees were disappointed at Annetts' resignation.
"The trustees have acted swiftly and will be appointing an interim chief executive to lead the organisation while a new permanent chief executive is recruited," she said.
"Trustees and the senior management team are working to manage the organisation and are committed to continuing the work recently started in developing the business of the organisation," the spokeswoman added.
Annetts was unavailable for comment.
Gill Tishler, YWCA's former chief executive, had been at the charity for 14 years when she stepped down in May.