brown #
= weekly rock chart peak
blue #
= pop chart peak
| 1 | Pretty Fly (For A White Guy) | 1 | 1 | 1-02-99 |  |
| The Offspring |
| 2 | Believe | 1 | 1-16-99 | |
| Cher |
| 3 | Angel | 1 | 2-06-99 | |
| Sarah McLachlan |
| 4 | Angel Of Mine | 1 | 2-13-99 | |
| Monica |
| 5 | Every Morning | 1 | 1 | 2-27-99 | |
| Sugar Ray |
| 6 | Stay The Same | 1 | 3-06-99 | |
| Joey McIntyre |
| 7 | No Scrubs | 1 | 3-20-99 | |
| TLC |
| 8 | Kiss Me | 1 | 4-03-99 | |
| Sixpence None The Richer |
| 9 | The Hardest Thing | 1 | 4-10-99 | |
| 98 Degrees |
| 10 | Thinking Of You (I Drive Myself Crazy) | 1 | 4-24-99 | |
| 'NSYNC |
| 11 | Livin' La Vida Loca | 1 | 5-01-99 | |
| Ricky Martin |
| 12 | I Want It That Way | 1 | 5-22-99 | |
| Backstreet Boys |
| 13 | If You Had My Love | 1 | 5-29-99 | |
| Jennifer Lopez |
| 14 | Wild Wild West | 1 | 6-19-99 | |
| Will Smith Featuring Dru Hill And Kool Moe Dee |
| 15 | Summer Girls | 1 | 7-03-99 | |
| LFO |
| 16 | All Star | 1 | 1 | 7-10-99 | |
| Smash Mouth |
| 17 | Genie In A Bottle | 1 | 7-24-99 | |
| Christina Aguilera |
| 18 | Bailamos | 1 | 8-14-99 | |
| Enrique Iglesias |
| 19 | I Do (Cherish You) | 1 | 8-21-99 | |
| 98 Degrees |
| 20 | Music Of My Heart | 1 | 8-28-99 | |
| 'NSYNC & Gloria Estefan |
| 21 | Unpretty | 1 | 9-04-99 | |
| TLC |
| 22 | Smooth | 10 | 1 | 9-18-99 | |
| Santana Featuring Rob Thomas |
| 23 | Heartbreaker | 1 | 10-09-99 | |
| Mariah Carey Featuring Jay-Z |
| 24 | (You Drive Me) Crazy | 1 | 10-16-99 | |
| Britney Spears |
| 25 | Back At One | 1 | 10-30-99 | |
| Brian McKnight |
| 26 | Waiting For Tonight | 1 | 11-06-99 | |
| Jennifer Lopez |
| 27 | I Wanna Love You Forever | 1 | 11-13-99 | |
| Jessica Simpson |
| 28 | I Knew I Loved You | 1 | 11-27-99 | |
| Savage Garden |
| 29 | Blue (Da Ba Dee) | 1 | 12-04-99 | |
| Eiffel 65 |
| 30 | What A Girl Wants | 1 | 12-25-99 | |
| Christina Aguilera |