The Portuguese takes the reins at the Ligue 2 side to become the first woman to take charge of a professional club in France
The 36-year-old Portuguese will replace Regis Brouard at the helm this summer having previously worked with Benfica, Celtic and the Iran women's national team.
"Clermont Foot 63 has chosen its new coach for next season in the person of Helena Costa," a statement on the club's official website reads.
"Costa previously worked at Benfica, Ovidelas and with the women national teams of Qatar and Iran, while also working with Celtic.
"This appointment is the start of a new era for Clermont, with 17 players under contract who will be joined by a number of youngsters from within the club."
A graduate in sports science, Costa was appointed as the Iran team boss in 2012 following two years at the forefront of women's football in Qatar.
The Alhandra-born coach also spent the early part of her career with the Benfica youth sides and lifted a regional league title with men's side Sociedade Recreativa e Desportiva Cheleirense.
Clermont currently sit 14th in Ligue 2 with 45 points from 36 games.