Fairuza's mother, Cathryn Balk, has studied, performed, and taught the ethnic and traditional dance forms of many countries such as Egypt, Turkey, Morocco and Spain. Her father, Solomon Feldthouse, was one of the founding members of the 1960s psychedelic rock group Kaleidoscope, and is also a traveling folk musician. He was born in Pingree, Idaho and between the ages of 6 and 10, he lived in Turkey where he learned Greek, Turkish, Iraqi and Iranian music. Balk has stated that her father is of Romani and Cherokee ancestry, and that her mother is of Irish and French descent.

Balk's debut role was in a television film titled The Best Christmas Pageant Ever, produced in 1983. While in London, Balk was cast by Walt Disney Productions to star as Dorothy Gale in Return to Oz, the unofficial sequel to MGM's 1939 musical The Wizard of Oz. This role led to other, minor roles, including that of Mildred Hubble in The Worst Witch, and in 1988, at age 14, she moved to Paris to work on Valmont with Miloš Forman. By 1989 she was back in Vancouver, where she attended high school. However, she soon decided to take correspondence courses instead and went back to Hollywood, where she gained increasing notice as an Actress. In 1992 she was awarded an Independent Spirit Award as best Actress for her performance in the Allison Anders film Gas Food Lodging.

In 1996, she appeared in a lead role in The Craft, in which her character formed a teenage coven with characters portrayed by Neve Campbell, Rachel True and Robin Tunney. Since then, Balk has continued to find roles, primarily dark ones. In 1996, she co-starred in The Island of Dr Moreau. In 1998, played a neo-Nazi goth-punk opposite Edward Norton in American History X, and was featured in The Waterboy, alongside Adam Sandler. Since 2000, she has appeared in over a dozen films. She has also done voice work for animated films, TV shows and video games, including Justice League, Family Guy, Grand Theft Auto: Vice City and Lords of EverQuest. The 2007 documentary Return to Oz: The Joy That Got Away was dedicated to her.

In 2010, Balk released the single "Stormwinds" under the Artist title "Armed Love Militia".

In 2011, Balk began to exhibit art in Los Angeles and New York. On August 4, 2012, she participated in the group show 'MiXTAPE', with other notable artists Mark Ryden, Camille Rose Garcia, Jessicka Addams, and Marion Peck. Artists were asked to pick a song and create art inspired by that song. Fairuza chose the song “Nuages” by Django Reinhardt and created a 16"x20"x12" mixed-media sculpture. The eclectic mix of songs chosen were featured for digital download on iTunes.

In 2017, the emo puppet band Fragile Rock performed a song entitled "Fairuza Balk" on their NPR Tiny Desk Concert. Balk tweeted that the song was "wonderful and hilarious" and made her year.