These are the UK Official Indie Chart number-one hits of the 1990 as compiled by MRIB and Music Week from August 11.
| Issue date | Song | Artist | Record label | ref |
|---|---|---|---|---|
| 6 January | "Getting Away with It" | Electronic | Factory | |
| 13 January | "Madchester Rave On" E.P. | Happy Mondays | ||
| 20 January | ||||
| 27 January | ||||
| 3 February | "Ride" E.P. | Ride | Creation | |
| 10 February | "Sleep With Me" | Birdland | Lazy | |
| 17 February | "Indian Rope" | The Charlatans | Situation Two | |
| 24 February | "Enjoy the Silence" | Depeche Mode | Mute | |
| 3 March | ||||
| 10 March | "Elephant Stone" | The Stone Roses | Silvertone | |
| 17 March | "Blue Savannah" | Erasure | Mute | |
| 24 March | ||||
| 8 April | "This Is How It Feels" | Inspiral Carpets | Cow | |
| 15 April | "Step On" | Happy Mondays | Factory | |
| 22 April | ||||
| 29 April | ||||
| 5 May | ||||
| 12 May | ||||
| 19 May | "Glider EP" | My Bloody Valentine | Creation | |
| 26 May | "Better the Devil You Know" | Kylie Minogue | PWL | |
| 2 June | ||||
| 9 June | "The Only One I Know" | The Charlatans | Situation Two | |
| 16 June | ||||
| 23 June | "World in Motion" | EnglandNew Order | Factory | |
| 30 June | "She Comes in the Fall" | Inspiral Carpets | Cow | |
| 7 July | ||||
| 14 July | "One Love" | The Stone Roses | Silvertone | |
| 21 July | ||||
| 28 July | ||||
| 4 August | "Velouria" | Pixies | 4AD | |
| 11 August | "Naked in the Rain" | Blue Pearl | Big Life | |
| 18 August | ||||
| 25 August | ||||
| 1 September | ||||
| 8 September | "What Time Is Love?" | The KLF | KLF Communications | |
| 15 September | ||||
| 22 September | ||||
| 29 September | ||||
| 6 October | "Groovy Train" | The Farm | Produce | |
| 13 October | "I Can't Stand It!" | Twenty 4 Seven | Freaky | |
| 20 October | ||||
| 27 October | ||||
| 3 November | "Kinky Afro" | Happy Mondays | Factory | |
| 10 November | ||||
| 17 November | "Step Back in Time" | Kylie Minogue | PWL | |
| 24 November | ||||
| 1 December | Island Head EP | Inspiral Carpets | Cow/Mute | |
| 8 December | "Sucker DJ" | Dimples D. | FBI | |
| 15 December | "All Together Now" | The Farm | Produce | |
| 22 December | ||||
| 29 December |
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