Billboard Year-End Hot 100 singles of 1999
This is a list of Billboard magazine's Top Hot 100 songs of 1999.
| № | Title | Artist |
| 1 | "Believe" | Cher |
| 2 | "No Scrubs" | TLC |
| 3 | "Angel of Mine" | Monica |
| 4 | "Heartbreak Hotel" | Whitney Houston featuring Faith Evans and Kelly Price |
| 5 | "...Baby One More Time" | Britney Spears |
| 6 | "Kiss Me" | Sixpence None the Richer |
| 7 | "Genie in a Bottle" | Christina Aguilera |
| 8 | "Every Morning" | Sugar Ray |
| 9 | "Nobody's Supposed to Be Here" | Deborah Cox |
| 10 | "Livin' la Vida Loca" | Ricky Martin |
| 11 | "Where My Girls At?" | 702 |
| 12 | "If You Had My Love" | Jennifer Lopez |
| 13 | "Slide" | Goo Goo Dolls |
| 14 | "Have You Ever?" | Brandy |
| 15 | "I Want It That Way" | Backstreet Boys |
| 16 | "I'm Your Angel" | R. Kelly and Celine Dion |
| 17 | "All Star" | Smash Mouth |
| 18 | "Angel" | Sarah McLachlan |
| 19 | "Smooth" | Santana featuring Rob Thomas |
| 20 | "Unpretty" | TLC |
| 21 | "Bills, Bills, Bills" | Destiny's Child |
| 22 | "Save Tonight" | Eagle-Eye Cherry |
| 23 | "Last Kiss" | Pearl Jam |
| 24 | "Fortunate" | Maxwell |
| 25 | "All I Have to Give" | Backstreet Boys |
| 26 | "Bailamos" | Enrique Iglesias |
| 27 | "What's It Gonna Be?!" | Busta Rhymes featuring Janet |
| 28 | "What It's Like" | Everlast |
| 29 | "Fly Away" | Lenny Kravitz |
| 30 | "Someday" | Sugar Ray |
| 31 | "Lately" | Divine |
| 32 | "That Don't Impress Me Much" | Shania Twain |
| 33 | "Wild Wild West" | Will Smith featuring Dru Hill and Kool Moe Dee |
| 34 | "Scar Tissue" | Red Hot Chili Peppers |
| 35 | "Heartbreaker" | Mariah Carey featuring Jay-Z |
| 36 | "I Still Believe" | Mariah Carey |
| 37 | "The Hardest Thing" | 98 Degrees |
| 38 | "Summer Girls" | LFO |
| 39 | "Can I Get A..." | Jay-Z featuring Amil and Ja Rule |
| 40 | "Jumper" | Third Eye Blind |
| 41 | "Doo Wop " | Lauryn Hill |
| 42 | "Mambo No. 5" | Lou Bega |
| 43 | "Sweet Lady" | Tyrese |
| 44 | "It's Not Right but It's Okay" | Whitney Houston |
| 45 | " A Little More Time on You" | 'N Sync |
| 46 | "Lullaby" | Shawn Mullins |
| 47 | "Anywhere" | 112 featuring Lil Zane |
| 48 | "Tell Me It's Real" | K-Ci & JoJo |
| 49 | "Back 2 Good" | Matchbox 20 |
| 50 | "808" | Blaque |
| 51 | "She's So High" | Tal Bachman |
| 52 | "She's All I Ever Had" | Ricky Martin |
| 53 | "Miami" | Will Smith |
| 54 | "Hands" | Jewel |
| 55 | "Who Dat" | JT Money featuring Solé |
| 56 | "Please Remember Me" | Tim McGraw |
| 57 | "From This Moment On" | Shania Twain |
| 58 | "Love Like This" | Faith Evans |
| 59 | "You" | Jesse Powell |
| 60 | "Trippin'" | Total featuring Missy Elliott |
| 61 | "If You" | Silk |
| 62 | "Ex-Factor" | Lauryn Hill |
| 63 | "Give It to You" | Jordan Knight |
| 64 | "Black Balloon" | Goo Goo Dolls |
| 65 | "Spend My Life with You" | Eric Benét featuring Tamia |
| 66 | "These Are the Times" | Dru Hill |
| 67 | "I Don't Want to Miss a Thing" | Mark Chesnutt |
| 68 | "I Do " | 98 Degrees |
| 69 | "Because of You" | 98 Degrees |
| 70 | "I Will Remember You" | Sarah McLachlan |
| 71 | "Chanté's Got a Man" | Chanté Moore |
| 72 | "Happily Ever After" | Case |
| 73 | "My Love Is Your Love" | Whitney Houston |
| 74 | "All Night Long" | Faith Evans featuring Puff Daddy |
| 75 | "Back That Azz Up" | Juvenile featuring Mannie Fresh and Lil Wayne |
| 76 | "Almost Doesn't Count" | Brandy |
| 77 | "Man! I Feel Like a Woman!" | Shania Twain |
| 78 | "Steal My Sunshine" | Len |
| 79 | "I Need to Know" | Marc Anthony |
| 80 | "So Anxious" | Ginuwine |
| 81 | "Faded Pictures" | Case featuring Joe |
| 82 | "Back at One" | Brian McKnight |
| 83 | "When a Woman's Fed Up" | R. Kelly |
| 84 | "How Forever Feels" | Kenny Chesney |
| 85 | "Amazed" | Lonestar |
| 86 | "Sometimes" | Britney Spears |
| 87 | "Ghetto Cowboy" | Mo Thugs |
| 88 | "Out of My Head" | Fastball |
| 89 | "Hard Knock Life " | Jay-Z |
| 90 | "Jamboree" | Naughty by Nature featuring Zhané |
| 91 | "Take Me There" | Blackstreet featuring Mýa, Mase and Blinky Blink |
| 92 | "Stay the Same" | Joey McIntyre |
| 93 | "A Lesson in Leavin'" | Jo Dee Messina |
| 94 | "Iris" | Goo Goo Dolls |
| 95 | "Satisfy You" | Puff Daddy featuring R. Kelly |
| 96 | "Better Days " | Citizen King |
| 97 | "Music of My Heart" | 'N Sync and Gloria Estefan |
| 98 | "Write This Down" | George Strait |
| 99 | "When You Believe" | Whitney Houston and Mariah Carey |
| 100 | " A Little More Time on You" | Alabama and 'N Sync |