She graduated from Brown University in 1983, where she met fellow alums Director Todd Haynes and Barry Ellsworth. Together, they created Apparatus Productions in 1987, a non-profit company deeply inspired by the anti-Hollywood New York film scene and oversaw the production of seven films in five years. Most notoriously, Apparatus produced Haynes' controversial Superstar: The Karen Carpenter Story, a film depicting the dramatic rise and fall of the anorexic pop star. To make financial ends meet, Vachon became a proofreader by night. She also took on odd jobs in the film industry to learn the trade.

Her first feature Poison (written and directed by Academy Award nominee Todd Haynes) won the Grand Jury Prize at Sundance in 1991. Since that initial success Christine has worked on a number of noteworthy films, including I Shot Andy Warhol, Happiness, Kids, One Hour Photo, and Boys Don't Cry. Through her enduring relationship with Todd, she has worked on every feature film of his to date, including Safe, Velvet Goldmine, Far From Heaven, and I'm Not There, which starred Christian Bale, Cate Blanchett, Richard Gere, Heath Ledger, Charlotte Gainsbourg, Julianne Moore, and Michelle Williams. Cate Blanchett received both Academy Award and SAG Award nominations for Best Supporting Actress, and the film was also nominated for 4 Independent Spirit Awards, notching a Best Supporting Actress win for Cate Blanchett.

Vachon and fellow New York Producer Pamela Koffler currently run Killer Films, which was established in 1996. The company celebrated its 10th anniversary in 2005 and was honored with a retrospective at the Museum of Modern Art in New York.

Killer's releases for 2008 include Savage Grace, directed by Tom Kalin and starring Julianne Moore; An American Crime, starring Catherine Keener and Ellen Page, directed by Tommy O'Haver: Then She Found Me, the directorial debut of Helen Hunt, starring herself, Bette Midler, Colin Firth and Matthew Broderick.

Vachon and her partner, Artist Marlene McCarty, live in the East Village of New York with their daughter Guthrie. In the fall of 2009, Vachon went into remission after a battle with breast cancer. She is related to the French costume designer, Sarah Monfort.

Vachon continued her long-standing collaboration with Todd Haynes for the 2015 film, Carol.