Costa, 36, will become the first female coach of a French professional club, and the first woman to manage in the top two divisions of a major European league.
Until now, such an appointment had only existed in the realms of fiction.
Announcing the appointment on Wednesday, a statement on Clermont’s website confirmed that Costa – who was most recently coach of the Iran women’s team – will be introduced to the media after this season’s final fixtures have been completed.
“Clermont Foot 63 has chosen Helena Costa to be our new coach,” read the statement.
“Helena Costa came through the ranks at Benfica before taking charge of the women’s teams at Odivelas, then the national teams of Qatar and Iran, in addition to working as a scout for Celtic.
“This appointment will allow Clermont Foot 63 to begin a new era, relying on a group of 17 players currently under contract, which will be added young players from the club.”
A graduate in sports science, Costa was appointed as the Iran team boss in 2012 following two years at working in women’s football in Qatar.
The Alhandra-born coach also spent the early part of her career with the Benfica youth sides and won a regional league title with men’s side Sociedade Recreativa e Desportiva Cheleirense.
Clermont are 14th in Ligue 2 with two matches to go.