List of UK Independent Singles Chart number ones of 1999
# List of UK Independent Singles Chart number ones of 1999

These are the Official Charts Company's UK Official Indie Chart number-one hits of 1999.

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