The 48-year-old actress and 56-year-old director announced their separation in a statement to People on Tuesday. Carter and Burton were together for 13 year, and have two children, 11-year-old son Billy and 7-year-old daughter Nell.
"[The couple] separated amicably earlier this year and have continued to be friends and co-parent their children," Carter's rep told the magazine. "We would ask that you respect their privacy and that of their children during this time."
Carter and Burton met on the set of Planet of the Apes in 2001. The actress would go on to star in a number of the director's other films, including Big Fish (2003), Sweeney Todd: The Demon Barber of Fleet Street (2007) and Alice in Wonderland (2010).
Carter will appear as the Fairy Godmother in a live-action Disney adaptation of Cinderella, and reprise the Red Queen for Burton film Alice in Wonderland: Through the Looking Glass in 2015. The director will next release Big Eyes with Amy Adams and Christoph Waltz on Dec. 25.