Dunst was born in Point Pleasant, New Jersey, to Klaus and Inez Dunst. Dunst's parents are separated; her father, Klaus Dunst, a German medical services executive, remained in New Jersey. Her mother, Inez Dunst, a Swedish former art gallery owner, moved to California. Dunst has a younger brother, Christian, born in 1986.
Dunst graduated from Notre Dame High School, a private Catholic high school in Sherman Oaks, in 2000, but attended the Ranney School during her elementary years.
Dunst started dating fellow actor Jake Gyllenhaal in September 2002, after meeting him through his sister, Maggie Gyllenhaal (her co-star in Mona Lisa Smile). They broke up in July 2004 and have been on-again, off-again since.