These are the Billboard magazine R&B singles chart number one hits of 1999:
| † | Indicates best-charting R&B single of 1999[1] |
| Issue date | Song | Artist(s) |
|---|---|---|
| January 2 | "Nobody's Supposed to Be Here" | Deborah Cox |
| January 9 | ||
| January 16 | ||
| January 23 | ||
| January 30 | ||
| February 6 | ||
| February 13 | "Heartbreak Hotel" | Whitney Houston featuring Faith Evans and Kelly Price |
| February 20 | ||
| February 27 | ||
| March 6 | ||
| March 13 | ||
| March 20 | ||
| March 27 | ||
| April 3 | "What's It Gonna Be?!" | Busta Rhymes featuring Janet Jackson |
| April 10 | "No Scrubs" | TLC |
| April 17 | ||
| April 24 | ||
| May 1 | ||
| May 8 | ||
| May 15 | "Fortunate" † | Maxwell |
| May 22 | ||
| May 29 | ||
| June 5 | ||
| June 12 | ||
| June 19 | ||
| June 26 | ||
| July 3 | ||
| July 10 | "Bills, Bills, Bills" | Destiny's Child |
| July 17 | ||
| July 24 | ||
| July 31 | ||
| August 7 | ||
| August 14 | ||
| August 21 | ||
| August 28 | ||
| September 4 | ||
| September 11 | "Never Gonna Let You Go" | Faith Evans |
| September 18 | "Spend My Life with You" | Eric Benet featuring Tamia |
| September 25 | ||
| October 2 | "We Can't Be Friends" | Deborah Cox featuring R.L. |
| October 9 | "Heartbreaker" | Mariah Carey featuring Jay-Z |
| October 16 | ||
| October 23 | "We Can't Be Friends" | Deborah Cox featuring R.L. |
| October 30 | "Satisfy You" | Puff Daddy featuring R. Kelly |
| November 6 | ||
| November 13 | "U Know What's Up" | Donell Jones featuring Lisa "Left Eye" Lopes |
| November 20 | ||
| November 27 | ||
| December 4 | ||
| December 11 | ||
| December 18 | ||
| December 25 |
