| Title | Details | Peak | Certification |
| AUS |
| Grandpaw Would | Released: 22 June 1995 Label: Fellaheen | — | |
| Something to Remember Me By | Released: 20 May 1997 Label: Fellaheen | — | |
| Breathing Tornados | Released: 16 November 1998 Label: Modular | 13 | ARIA: Gold |
| hey you. yes you. | Released: 15 November 2002 Label: Modular | 45 | |
| Awake Is the New Sleep | Released: 22 February 2005 Label: Ten Fingers | 5 | ARIA: 2× Platinum |
| Ripe | Released: 18 September 2007 Label: Ten Fingers | 11 | ARIA: Gold |
| The Rebirth of Venus | Released: 6 February 2009 Label: Dew Process | 21 | |
| Deeper into Dream | Released: 11 October 2011 Label: Dew Process | — | |
| Ayahuasca: Welcome to the Work | Released: 22 April 2013 Label: Ten Fingers | — | |
| Love Is the Great Rebellion | Released: 29 May 2015 Label: Warner Bros. | 71 | |
| Freedom, Love and the Recuperation of the Human Mind | Released: 21 October 2016 Label: Ben Lee, ABC Music | — | |
| Ben Lee Sings Songs About Islam for the Whole Family | Released: 3 March 2017 | — | |
| Quarter Century Classix | Released: 22 November 2019 Label: New West | — | |
| I'm Fun! | Released: 19 August 2022 Label: Warner Music Australia | 46 | |
| This One's for the Old Headz | Released: 20 September 2024 Label: Weirder Together | — |