These are the Official Charts Company's UK Indie Chart number-one albums of 2006.
| Issue date | Album | Artist(s) | Record label | Ref. |
|---|---|---|---|---|
| 1 January | The Singles | Basement Jaxx | XL | [1] |
| 8 January | First Impressions of Earth | The Strokes | Rough Trade | [2] |
| 15 January | [3] | |||
| 22 January | Veneer | José González | Imperial Recordings | [4] |
| 29 January | Whatever People Say I Am, That's What I'm Not | Arctic Monkeys | Domino | [5] |
| 5 February | [6] | |||
| 12 February | [7] | |||
| 19 February | [8] | |||
| 26 February | [9] | |||
| 5 March | [10] | |||
| 12 March | [11] | |||
| 19 March | [12] | |||
| 26 March | [13] | |||
| 2 April | This New Day | Embrace | Independiente | [14] |
| 9 April | Ringleader of the Tormentors | Morrissey | Attack | [15] |
| 16 April | [16] | |||
| 23 April | Simpatico | The Charlatans | Creole | [17] |
| 30 April | Whatever People Say I Am, That's What I'm Not | Arctic Monkeys | Domino | [18] |
| 7 May | [19] | |||
| 14 May | [20] | |||
| 21 May | Broken Boy Soldiers | The Raconteurs | XL | [21] |
| 28 May | [22] | |||
| 4 June | [23] | |||
| 11 June | [24] | |||
| 18 June | Catch-Flame! | Paul Weller | Yep Roc | [25] |
| 25 June | The Greatest Hits – Why Try Harder | Fatboy Slim | Skint | [26] |
| 2 July | Liberation Transmission | Lostprophets | Visible Noise | [27] |
| 9 July | [28] | |||
| 16 July | The Eraser | Thom Yorke | XL | [29] |
| 23 July | [30] | |||
| 30 July | The Greatest Hits – Why Try Harder | Fatboy Slim | Skint | [31] |
| 6 August | [32] | |||
| 13 August | Broken Boy Soldiers | The Raconteurs | XL | [33] |
| 20 August | [34] | |||
| 27 August | Never Said Goodbye | Cerys Matthews | Rough Trade | [35] |
| 3 September | Whatever People Say I Am, That's What I'm Not | Arctic Monkeys | Domino | [36] |
| 10 September | Crazy Itch Radio | Basement Jaxx | XL | [37] |
| 17 September | Whatever People Say I Am, That's What I'm Not | Arctic Monkeys | Domino | [38] |
| 24 September | The Greatest Hits – Why Try Harder | Fatboy Slim | Skint | [39] |
| 1 October | [40] | |||
| 8 October | [41] | |||
| 15 October | Yours to Keep | Albert Hammond Jr. | Rough Trade | [42] |
| 22 October | Broken Boy Soldiers | The Raconteurs | XL | [43] |
| 29 October | [44] | |||
| 5 November | So This Is Great Britain? | The Holloways | TVT | [45] |
| 12 November | Someone to Drive You Home | The Long Blondes | Rough Trade | [46] |
| 19 November | Jarvis | Jarvis Cocker | [47] | |
| 26 November | Orphans: Brawlers, Bawlers & Bastards | Tom Waits | Anti | [48] |
| 3 December | Jarvis | Jarvis Cocker | Rough Trade | [49] |
| 10 December | Piece by Piece | Katie Melua | Dramatico | [50] |
| 17 December | [51] | |||
| 24 December | [52] | |||
| 31 December | Hold Your Colour | Pendulum | Breakbeat Kaos | [53] |