| Rank | Game | Copies Sold | |
|---|
| 1 |
| Super Mario 64 | 11,000,000 | |
| 2 |
| Mario Kart 64 | 8,470,000 | |
| 3 |
| GoldenEye 007 | 8,000,000 | |
| 4 |
| The Legend of Zelda: Ocarina of Time | 7,600,000 | |
| 5 |
| Super Smash Bros | 4,900,000 | |
| 6 |
| Diddy Kong Racing | 4,434,000 | |
| 7 |
| Pokemon Stadium | 3,871,000 | |
| 8 |
| Donkey Kong 64 | 3,770,000 | |
| 9 |
| The Legend of Zelda: Majora's Mask | 3,360,000 | |
| 10 |
| Star Fox 64 | 3,325,000 | |
| 11 |
| Banjo-Tooie | 3,000,000 | |
| 12 |
| Pokemon Snap | 2,718,000 | |
| 13 |
| Perfect Dark | 2,500,000 | |
| 14 |
| Mario Party 2 | 2,330,000 | |
| 15 |
| Banjo-Kazooie | 2,256,000 | |
| 16 |
| Pokemon Stadium 2 | 2,150,000 | |
| 17 |
| Wave Race 64 | 2,105,000 | |
| 18 |
| Star Wars: Shadows of the Empire | 2,008,000 | |
| 19 |
| Yoshi's Story | 1,953,000 | |
| 20 |
| Mario Party | 1,944,000 | |
| 21 |
| WCW/nWo Revenge | 1,880,000 | |
| 22 |
| Star Wars: Episode I Racer | 1,798,000 | |
| 23 |
| Cruis'n USA | 1,680,000 | |
| 24 |
| Star Wars: Rogue Squadron | 1,634,000 | |
| 25 |
| Tony Hawk's Pro Skater | 1,610,000 | |
| 27 |
| WCW vs. nWo: World Tour | 1,300,000 | |
| 28 |
| 1080 Snowboarding | 1,254,000 | |
| 29 |
| WWF No Mercy | 1,190,000 | |
| 30 |
| Turok 2: Seeds of Evil | 1,154,000 | |
| 31 |
| WWF WrestleMania 2000 | 1,140,000 | |
| 32 |
| Mario Tennis | 1,100,000 | |
| 33 |
| The World Is Not Enough | 1,080,000 | |
| 34 |
| Kirby 64: The Crystal Shards | 1,070,000 | |
| 35 |
| Namco Museum 64 | 1,040,000 | |
| 36 |
| Mario Party 3 | 1,020,000 | |
| 37 |
| Kobe Bryant in NBA Courtside | 1,000,000 | |
| 38 |
| PilotWings 64 | 1,000,000 | |
| 39 |
| Turok: Dinosaur Hunter | 1,000,000 | |