"Helena Costa has decided not to keep her commitments to Clermont and she will therefore not be the club's coach next season," the Ligue 2 club's president, Claude Michy, said in a statement on Monday.
"This is a sudden and disappointing decision."
As yet no reason for her surprising decision has been given.
Portuguese Costa, 36, had previously coached the Iran women's national team and scouted for Scottish Premier League club Celtic.
No woman had come as close as Costa to coaching a top men's professional team in Europe, and on accepting the job last month she sounded bullish in the face of intense media interest.
"I'm not afraid," she said at her first news conference. "If I didn't think I'm capable of this, I wouldn't be here. If I didn't think the players would accept me, and if I didn't believe in my work, I wouldn't be here."
The pressures of which she spoke are not to be underestimated, since women in similar situations have ended up walking away.
Carolina Morace was appointed coach of Serie C1 (third division) club Viterbese in Italy in 1999, for example, but resigned after two matches citing media pressure.
Other women have succeeded long term in football, including West Ham chief executive Karren Brady, who has held top-level jobs in football club administration since 1993.
Referee Bibiana Steinhaus officiates in German second division games. She is the first female referee in Bundesliga 2 and the first to have been a referee in the German Cup.
Maria Jose Claramunt is the director of Spain's national team, responsible more for marketing than sporting issues, and in England Karren Brady is the former managing director of Birmingham City and is now the vice chairman of Premier League West Ham United.
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- Helena Costa