Lee was born to parents John Lee, a disc jockey and TV personality, and Sara Cargill. She has one brother, Robby, and two sisters, Carrie and Lori. Lee had a third sister, who died in 1987 at the age of three from an unidentified illness. The song "Hello" from Fallen has been reported to have been written for her late sister, as well as the song "Like You" from The Open Door with the lyrics, "I long to be like you, sis; Lie cold in the ground like you did," also hinting at the death of her sister and her grief for it. Lee took classical piano lessons for nine years. Her family moved to many places, including Florida and Illinois, but eventually settled in Little Rock, Arkansas, where Evanescence started. She graduated from Pulaski Academy in 2000 and also briefly attended Middle Tennessee State University. Lee has stated that she is of mostly Scottish and English heritage.

In an interview on AOL Music, Lee revealed that the first songs she remembered writing were called "Etern