This is a list of songs which reached number one on the Billboard Mainstream Top 40 chart in 2006.
During 2006, a total of 15 singles hit number-one on the charts.
| Issue date | Song | Artist(s) | Ref. |
|---|---|---|---|
| January 7 | "Run It!" | Chris Brown | [1] |
| January 14 | |||
| January 21 | |||
| January 28 | "Stickwitu" | The Pussycat Dolls | |
| February 4 | |||
| February 11 | "Check on It" | Beyoncé featuring Slim Thug | |
| February 18 | |||
| February 25 | |||
| March 4 | |||
| March 11 | |||
| March 18 | |||
| March 25 | "So Sick" | Ne-Yo | |
| April 1 | "Be Without You" | Mary J. Blige | |
| April 8 | |||
| April 15 | |||
| April 22 | |||
| April 29 | "Temperature" | Sean Paul | |
| May 6 | |||
| May 13 | "SOS" | Rihanna | |
| May 20 | "Temperature" | Sean Paul | |
| May 27 | "Hips Don't Lie" | Shakira featuring Wyclef Jean | |
| June 3 | |||
| June 10 | |||
| June 17 | |||
| June 24 | |||
| July 1 | |||
| July 8 | |||
| July 15 | bgcolor=#FFFF99 rowspan="8" | "Promiscuous" | Nelly Furtado featuring Timbaland |
| July 22 | |||
| July 29 | |||
| August 5 | |||
| August 12 | |||
| August 19 | |||
| August 26 | |||
| September 2 | |||
| September 9 | "Buttons" | The Pussycat Dolls featuring Snoop Dogg | |
| September 16 | |||
| September 23 | "SexyBack" | Justin Timberlake | |
| September 30 | |||
| October 7 | |||
| October 14 | |||
| October 21 | |||
| October 28 | "Far Away" | Nickelback | |
| November 4 | |||
| November 11 | "Lips of an Angel" | Hinder | |
| November 18 | |||
| November 25 | |||
| December 2 | "My Love" | Justin Timberlake featuring T.I. | |
| December 9 | |||
| December 16 | |||
| December 23 | |||
| December 30 | "Irreplaceable" | Beyoncé | |