Primark chief Paul Marchant announced his resignation with immediate effect on Monday after allegations that he behaved inappropriately towards a woman "in a social environment."
The parent company, Associated British Foods, said Marchant cooperated with an investigation led by external lawyers and acknowledged his "error of judgement."
"I am immensely disappointed," said CEO George Weston.
"Acting responsibly is the only way to build and manage a business over the long term. Colleagues and others must be treated with respect and dignity. Our culture has to be, and is, bigger than any one individual."
Marchant apologized to the accuser, colleagues, and the company board.
ABF's chief financial officer has been tapped to step in as interim CEO.
Low cost, high controversy
Marchant had led Primark since 2009, the same year the stores first entered the German market.
The Irish chain operates more than 450 stores in 17 countries across Europe and the United States.
Primark has expanded thanks to its extremely low prices and chic presentation. But its low prices have also attracted controversy.
The fast fashion brand has previously come under fire for poor working conditions in their manufacturing facilities. It was one of the brands that was linked to the Bangladeshi textile factory that collapsed in 2013, killing more than 1,000 people.
Edited by: Zac Crellin