These are the Official Charts Company's UK Official Indie Chart number-one hits of 1999. [1]
| Issue date | Song | Artist |
|---|---|---|
| 2 January | "Heartbeat/Tragedy" | Steps |
| 9 January [a] | ||
| 16 January [a] | "Praise You" | Fatboy Slim |
| 23 January | ||
| 30 January | "Heartbeat/Tragedy" | Steps |
| 6 February | "Good Life (Buena Vida)" | Inner City |
| 13 February | "Heartbeat/Tragedy" | Steps |
| 20 February | "Changes" | 2Pac |
| 27 February [a] | "...Baby One More Time" | Britney Spears |
| 6 March | ||
| 13 March | ||
| 20 March | "Better Best Forgotten" | Steps |
| 27 March | "...Baby One More Time" | Britney Spears |
| 3 April [a] | "Flat Beat" | Mr. Oizo |
| 10 April | ||
| 17 April | ||
| 24 April | "Electricity" | Suede |
| 1 May | "Right Here, Right Now" | Fatboy Slim |
| 8 May | "Red Alert" | Basement Jaxx |
| 15 May [a] | "I Want It That Way" | Backstreet Boys |
| 22 May | ||
| 29 May | ||
| 5 June [a] | "Sweet like Chocolate" | Shanks & Bigfoot |
| 12 June [a] | ||
| 19 June | ||
| 26 June | "Sometimes" | Britney Spears |
| 3 July | ||
| 10 July | ||
| 17 July | ||
| 24 July | "Love's Got a Hold on My Heart" | Steps |
| 31 July | ||
| 7 August | "Straight from the Heart" | Doolally |
| 14 August | "Rendez-Vu" | Basement Jaxx |
| 21 August | ||
| 28 August | "King of Snake" | Underworld |
| 4 September | "Sing It Back" | Moloko |
| 11 September | ||
| 18 September | ||
| 25 September | "Sun Is Shining" | Bob Marley vs. Funkstar De Luxe |
| 2 October | ||
| 9 October | ||
| 16 October | ||
| 23 October | "Going Underground/Carnation" | Buffalo Tom/Liam Gallagher |
| 30 October | "If I Could Turn Back the Hands of Time" | R. Kelly |
| 6 November | ||
| 13 November | ||
| 20 November | "Hurry Up and Wait" | Stereophonics |
| 27 November | "The Millennium Prayer" | Cliff Richard |
| 4 December [a] | ||
| 11 December [a] | ||
| 18 December [a] | ||
| 25 December |