Carpenter was born in Louisville, Kentucky, the daughter of Catherine (née Mitchell) and Robert Carpenter. She attended St. Raphael the Archangel and then Sacred Heart Academy. She trained at the Walden Theatre Conservatory program, and later at New York City's Juilliard School (Drama Division Group 31: 1998–2002). Before graduation, she was cast in the 2002 Broadway revival of Arthur Miller's The Crucible starring Liam Neeson and Laura Linney.
Carpenter first attracted critical attention for her performance in The Exorcism of Emily Rose. She took home the 2006 MTV Movie Award for 'Best Frightened Performance', and also received a 'Hollywood Life Breakthrough Award'. She was also named 'Breakout Performer' at the 2006 Scream Awards.
In 2008 she also starred in Quarantine a horror film about a deadly virus outbreak.
Carpenter played the role of Debra Morgan in the Showtime crime drama television series Dexter, which premiered October 1, 2006. Her portrayal of the title character's adoptive sister has impressed some critics, with Australian journalist Jack Marx describing her portrayal of "cool and clumsy" Debra as "so perfect that many viewers appear to have mistaken the character's flaws for the actor's."
In 2011, she starred in the off-Broadway play Gruesome Playground Injuries at Second Stage Theatre and had a guest appearance on the CBS drama The Good Wife.
In January 2014, it was announced that Carpenter would star in a new ABC drama Sea of Fire, playing FBI Agent Leah Pierce. However, the show was not picked up as a series. In August 2014, it was announced that she would provide the voice of Juli Kidman in the survival horror video game The Evil Within, marking her first video game appearance. The game was released in October 2014.
In early 2015, Carpenter was cast in the CBS drama series Limitless in which she co-starred with Jake McDorman.
In 2007, she began dating her Dexter co-star Michael C. Hall. They eloped on New Year's Eve, 2008 in California and publicly appeared together for the first time as a married couple at the 66th Golden Globe Awards in January 2009. In December 2010, Hall and Carpenter released a statement announcing that they had filed for divorce after having been separated "for some time". The divorce was finalized in December 2011 for irreconcilable differences; however, the two remain very close friends.
Carpenter started dating folk musician Seth Avett in 2013. On February 10, 2015, it was announced that the couple were engaged and expecting their first child. In August 2015, it was revealed that Carpenter gave birth in May to a son Isaac, and admitted that she was eight-and-a-half months pregnant when shooting the pilot episode of Limitless. Carpenter and Avett married in May 2016.
In 2010, she ran the New York City Marathon, completing it in 3:34:28.