Lee's musical career began in 1993 with the band Noise Addict, who were signed to Steve Pavlovic's independent label Fellaheen Records, on the strength of a self-produced and distributed four-track demo recorded in Lee's bedroom.

These included the acoustic Young and Jaded EP in 1994, which contained Lee's tribute to Evan Dando, "I Wish I Was Him".

In 2009, Lee recorded a new Noise Addict album, It Was Never About the Audience, with a new lineup: Lou Barlow and Lara Meyerratken.

He began recording his first solo album, Grandpaw Would, in both Sydney and Chicago with producer Brad Wood.

An alternate version of his song "Burn to Shine", produced by T-Bone Burnett, played over the end credits of the film Best Men.

1998's Breathing Tornados, released on Pavlovic's new label Modular, marked a new direction for Lee as he introduced synthesisers and increased instrumentation into his sound.

The first release on the label was the single, "Gamble Everything for Love", followed by the album, Awake Is the New Sleep in February 2005, which went double platinum in Australia.

A defining release in his career, the album showcased a much brighter, positive side of Lee's personality, in contrast to his previous darker musings.

Awake Is the New Sleep received several nominations for the 2005 Australian Recording Industry Association (ARIA) awards, and Lee won Best Male Artist, Best Independent Release, and Single of the Year for "Catch My Disease", which Lee wrote with Mcgowan Southworth.

Lee released his sixth album, Ripe, on 18 September 2007, with Benji Madden and Mandy Moore making appearances.

[2] In February 2009, Lee released his seventh studio album, The Rebirth of Venus, which received mixed reviews.

[3] It featured guest performances from the likes of Missy Higgins and Patience Hodgson, and peaked at No.21 on the ARIA Charts.

In April 2013, Lee released his ninth and arguably his most experimental studio album, entitled Ayahuasca: Welcome to the Work,[5] with collaboration from Jessica Chapnik.

[6] In June 2015, Lee released his 10th solo album, Love Is the Great Rebellion, his first on a major label, Warner Bros.

[7] According to Radio National's Geoff Wood, Lee invented the term "electro-yoga" to describe a new form of music dedicated to the practice of yoga.

Lee released Quarter Century Classix in 2019, a collection of cover songs he was influenced by during his teenage years.