Sagnier was born in La Celle-Saint-Cloud, in the département of Yvelines; her mother is a retired secretary and her father is a professor of English at a Paris University. She started taking acting classes at a young age and made her film debut at age 10 in I Want to Go Home and Les maris, les femmes, les amants (both released in 1989).

In 2001, she was named one of the Shooting Stars by European Film Promotion. She was nominated for the César Award for Most Promising Actress in 8 Women (2002). Sagnier performed in two films in competition at the 2003 Cannes Film Festival, La Petite Lili and Swimming Pool, both released in the same year. Also in 2003, she won the Prix Romy Schneider.

Sagnier has appeared completely nude in extended scenes in several films, including Water Drops on Burning Rocks, Bon plan (both released in 2000), and La Petite Lili. In the Francois Ozon's film Swimming Pool, Sagnier appears topless for more than half the film. Addressing this issue, Sagnier told Playboy:

She also starred in P. J. Hogan's 2003 adaptation of Peter Pan, as Tinkerbell.

In 2005, she recorded a series of introductions for Sky Movies. These included intros to several films.

On 25 March 2005 she gave birth to a daughter named Bonnie. The father is actor Nicolas Duvauchelle.