Rosemary Gillespie, chief executive of the Terrence Higgins Trust for the past 15 months, has left the charity after it asked her to stand down with immediate effect.
The HIV and sexual health charity said in a statement that its board had decided "a change of leadership is needed for the next stage of the organisation's development".
A spokesman for the charity said Gillespie had not received any payments for her departure other than those associated with her standard contractual notice period.
But Gillespie told Third Sector she had been "treated shabbily" and that the charity's board "does not have the stomach for the programme of change I was brought in to deliver".
Gillespie, who had been asked to produce a new strategic plan for 2016 to 2020, said her removal came "out of the blue" and contrasted with what she said was a supportive email in April from Robert Glick, the charity's chair.
According to Gillespie, the email read: "I think you and I are on our way to developing an outstanding partnership, and I couldn't be more excited about working with you at the helm as we take the leap into the next stage of this great charity's work."
The charity declined to comment on Gillespie's claims.