Malone was born on November 21, 1984, in Sparks, Nevada, the daughter of Deborah Malone and Edward Berge. Her father is of partly Norwegian descent; she also has Irish ancestry. According to Malone, her mother became pregnant with her after a one-night stand with her father, who was married to another woman at the time. Malone was raised by her mother and her mother’s girlfriend. “They were lovers,” Malone has said. “I had two moms, and it was awesome.” She remained estranged from her father for much of her early life but reconciled with him in adulthood.

As a child, Malone first began taking an interest in acting while watching her mother perform in community theater in the Lake Tahoe area. In 1995 she moved to Las Vegas, where she resided with her family for nine months, and began taking acting classes while her mother worked in a call center. She subsequently persuaded her mother to move to Los Angeles so she could pursue an acting career. Malone has said that she and her mother struggled financially in Los Angeles. She was home-schooled from sixth to eighth grade and attended the Professional Children’s School in New York City for ninth grade. She has one younger maternal half-sister, Madison Mae Malone (born 1997).

Malone progressed to professional acting with the film Bastard Out of Carolina (1996). She was nominated at the 1996 Independent Spirit Awards for Best Debut Performance and at the third Screen Actors Guild Awards for Outstanding Performance by a Female Actor in a Television Movie or Miniseries for her role in the film. From there her roles grew to include several Hollywood features. In 1997 she was nominated for a Golden Globe Award in the category Best Actress in a Miniseries or Television Film for her role in the television film Hope (1997), portraying a young girl growing up in a small town in the 1960s.

After completing Hope Malone was cast in Robert Zemeckis’s science fiction film Contact (1997), playing the child counterpart of Jodie Foster’s lead character. For her portrayal she won a Saturn Award for Best Performance by a Younger Actor. The following year Malone was cast opposite Susan Sarandon and Julia Roberts in the drama Stepmom (1998), playing an adolescent girl whose father has remarried and whose mother is dying of terminal cancer. The film was a box office success, grossing over $150 million against a $50 million budget. In 1999 Malone filed for legal emancipation from her mother in a Los Angeles County Court, and subsequently alleged that her mother had mismanaged her earnings, spending $280,000 of her trust account. She was granted legal emancipation in January 2000. After dropping out of high school in 1999, Malone obtained a General Educational Development certificate in 2001.

In 2000, at age 15, after appearing in “Contact″ and “Stepmom,″ Jena Malone won legal emancipation from her mother after accusing the woman of squandering Ms. Malone’s earnings through “excessive spending and mismanagement,″ according to court papers.

Malone had her first cinematic leading role in the psychological science fiction thriller film Donnie Darko (2001), playing Gretchen Ross, the new girl in town who becomes the girlfriend of Jake Gyllenhaal’s title character. Though the film was not a box-office hit, it later gained notoriety as a cult film. The same year she had a supporting part in the drama Life as a House (2001), portraying the girlfriend of a young man (Hayden Christensen) whose ailing father (Kevin Kline) is building a home. Malone co-produced the independent comedy-drama American Girl (2002), the first feature in which she had top billing, co-starring with Brad Renfro and Alicia Witt as a suicidal young woman whose father is in prison. In 2002 Malone played the part of a Catholic schoolgirl with a painful secret opposite Emile Hirsch in The Dangerous Lives of Altar Boys, also featuring Vincent D’Onofrio and Jodie Foster. In 2003, Jena appeared as “ferry girl” in Cold Mountain.

In 2003, at age 19, Malone purchased a home in Lake Tahoe, Nevada, where she resided as of 2012.

In 2006 Malone made her Broadway stage debut as Sister James in a production of the Tony Award-winning play Doubt. Ben Brantley of The New York Times wrote that Malone “slides effortlessly and appealingly into the part of the dewy, impressionable Sister James.” She also appeared in films, co-starring with Chloë Sevigny in filmmaker M. Blash’s improvised feature Lying (2006), playing one of several women attending a precarious weekend gathering. Malone followed this with supporting roles in the independent comedy The Go-Getter (2007), playing a young woman reunited with her middle school crush, and the biographical drama Into the Wild (2007), in which she portrayed the sister of Chris McCandless.

In 2007 it was announced that Malone was releasing her first single on The Social Registry, a New York City experimental music label, as Jena Malone and the Bloodstains. A number of tracks were subsequently posted to her MySpace page. Pitchfork Media has described Malone’s music as “pretty out-there—bedroom electronics, spaced-out keyboards, and Malone’s spare vocals.” In 2008 she formed the musical project The Shoe, which features Malone performing with a series of electronic instruments contained within a steamer trunk. She began performing impromptu live shows on street corners in 2008.

Malone appeared in the supernatural horror film The Ruins (2008) opposite Shawn Ashmore and Jonathan Tucker, playing one of several backpackers in Mexico who become trapped on a Mayan temple teeming with vines that can animate and attack those who come into contact with them. The following year she returned to theater, portraying Lavinia in an off-Broadway revival of Eugene O’Neill’s play Mourning Becomes Electra, opposite Lili Taylor. In 2011 Malone played the role of Rocket in Zack Snyder’s action film Sucker Punch. The film’s commercial failure caused Malone to reevaluate her career and consider focusing on photography and music. After the success of her next role, in The History Channel’s miniseries Hatfields and McCoys, Malone’s passion for acting returned.

In 2012 Malone starred in Dakota, a series on the YouTube channel Wigs, portraying the title character. She was attached to play Carson McCullers in the film Lonely Hunter, directed by Deborah Kampmeir, and had a supporting role in the independent drama In Our Nature (2012) opposite Zach Gilford and Gabrielle Union, playing one of several young people on a couples’ getaway.

In 2013 Malone reunited with M. Blash and co-star Chloë Sevigny in the independent drama The Wait, portraying the sister of a woman who believes their dead mother will be resurrected. The same year she was cast as Johanna Mason in The Hunger Games: Catching Fire (2013).

In 2014 Malone exhibited 39 photographs she had taken in Myanmar that summer. The exhibition, which ran from November 21 to 28, was called “The Holy Other.” It took place at MAMA, an art gallery owned by Malone’s friend Adarsha Benjamin in Downtown Los Angeles. Proceeds were donated to Girl Determined, a nonprofit organization that benefits girls’ education in Myanmar. Also in 2014 Malone had a supporting role in Paul Thomas Anderson’s neo-noir film Inherent Vice (2014), portraying an ex-heroin addict who hires a detective (Joaquin Phoenix) to find her husband. Malone also reprised the role of Johanna Mason in two Hunger Games sequels, Mockingjay – Part 1 (2014) and Mockingjay – Part 2 (2015).

Malone was cast as Jenet Klyburn in Batman v Superman: Dawn of Justice, also directed by Zack Snyder. Her scenes were left out of the theatrical release but included on the “Ultimate Edition” home video release. In February 2015 Malone was cast alongside Elle Fanning in Nicolas Winding Refn’s horror film The Neon Demon, which focuses on an aspiring model in Los Angeles. The film garnered criticism for a scene in which Malone engages in necrophilia. The Telegraph’s Tim Robey deemed it the “most offensive film of the year” but conceded it was not “any fault of Malone’s, who commits herself utterly to making it an anguished, desperate, if inevitably revolting minute or so of screen time. It’s a question of context, and how this scene… slots into the film’s overall thesis.”

In May 2016 Malone gave birth to a son, Ode Mountain, with her boyfriend, photographer Ethan DeLorenzo. The couple announced their engagement on August 30, 2016. In February 2019, Malone and De Lorenzo ended their relationship.

Malone endorsed Senator Bernie Sanders in the 2016 U.S. presidential election.

Malone is credited as co-writer and featured vocalist on the Foster the People track “Static Space Lover” from the band’s third album, Sacred Hearts Club, released on July 21, 2017.