| Id | Title | Sales | Debut | Genre | Developer | Publisher |
|---|---|---|---|---|---|---|
| 1 | Mario Kart 7 † | 18.99 million[2] | December 1, 2011 | Racing | Nintendo EADRetro Studios | Nintendo |
| 2 | Pokémon X and Y † | 16.80 million[2] | October 12, 2013 | Role-playing | Game Freak | The Pokémon CompanyNintendo |
| 3 | Pokémon Sun and Moon | 16.34 million[2] | November 18, 2016 | Role-playing | Game Freak | The Pokémon CompanyNintendo |
| 4 | Pokémon Omega Ruby and Alpha Sapphire | 14.68 million[2] | November 21, 2014 | Role-playing | Game Freak | The Pokémon CompanyNintendo |
| 5 | New Super Mario Bros. 2 † | 13.42 million[2] | July 28, 2012 | Platform | Nintendo EAD | Nintendo |
| 6 | Animal Crossing: New Leaf † | 13.07 million[2] | November 8, 2012 | Life simulation | Nintendo EAD | Nintendo |
| 7 | Super Mario 3D Land † | 12.89 million[2] | November 3, 2011 | Platform | Nintendo EAD | Nintendo |
| 8 | Super Smash Bros. for Nintendo 3DS | 9.65 million[2] | September 13, 2014 | Fighting | Bandai Namco StudiosSora Ltd. | Nintendo |
| 9 | Pokémon Ultra Sun and Ultra Moon | 9.26 million[2] | November 17, 2017 | Role-playing | Game Freak | The Pokémon CompanyNintendo |
| 10 | Yo-kai Watch 2 | 7.30 million[3] | December 13, 2014 | Role-playing | Level-5 | .mw-parser-output .plainlist ol,.mw-parser-output .plainlist ul{line-height:inherit;list-style:none;margin:0;padding:0}.mw-parser-output .plainlist ol li,.mw-parser-output .plainlist ul li{margin-bottom:0}JP: Level-5WW: Nintendo |
| 11 | Tomodachi Life † | 6.73 million[2] | April 18, 2013 | Life simulation | Nintendo SPD | Nintendo |
| 12 | Luigi's Mansion: Dark Moon | 6.48 million[3] | March 20, 2013 | Action-adventure | Next Level Games | Nintendo |
| 13 | The Legend of Zelda: Ocarina of Time 3D † | 6.44 million[3] | June 16, 2011 | Action-adventure | Grezzo | Nintendo |
| 14 | Nintendogs + Cats | 4.69 million[3] | February 26, 2011 | Pet-raising simulation | Nintendo EAD | Nintendo |
| 15 | Monster Hunter Generations | 4.30 million[4] | November 28, 2015 | Action role-playing | Capcom | Capcom |
| 16 | The Legend of Zelda: A Link Between Worlds † | 4.26 million[3] | November 22, 2013 | Action-adventure | Nintendo EAD | Nintendo |
| 17 | Monster Hunter 4 Ultimate † | 4.20 million[4] | February 13, 2015 | Action role-playing | Capcom | Capcom |
| 18 | Monster Hunter 4 | 4.10 million[4] | September 14, 2013 | Action role-playing | Capcom | Capcom |
| 19 | Super Mario Maker for Nintendo 3DS | 3.79 million[5] | December 1, 2016 | Level editorplatform | Nintendo EAD | Nintendo |
| 20 | Animal Crossing: Happy Home Designer | 3.51 million[6] | July 2, 2015 | Life simulation | Nintendo EAD | Nintendo |
| 21 | The Legend of Zelda: Majora's Mask 3D | 3.46 million[3] | February 13, 2015 | Action-adventure | Grezzo | Nintendo |
| 22 | Fire Emblem Fates: Birthright and Conquest | 3.09 million[3] | June 25, 2015 | Tactical role-playing | Intelligent SystemsNintendo SPD | Nintendo |
| 23 | Yo-kai Watch † | 2.97 million[3] | July 11, 2013 | Role-playing | Level-5 | JP: Level-5WW: Nintendo |
| 24 | Mario Party: Island Tour | 2.95 million[5] | November 22, 2013 | Party | NDcube | Nintendo |
| 25 | Donkey Kong Country Returns 3D | 2.94 million[3] | May 24, 2013 | Platform | Retro StudiosMonster Games | Nintendo |
| 26 | Mario & Luigi: Dream Team † | 2.70 million[3] | July 12, 2013 | Role-playing | AlphaDreamGood-Feel | Nintendo |
| 27 | Kirby: Triple Deluxe | 2.66 million[3] | January 11, 2014 | Actionplatform | HAL Laboratory | Nintendo |
| 28 | Monster Hunter 3 Ultimate | 2.60 million[4] | December 10, 2011 | Action role-playing | Capcom | Capcom |
| 29 | Paper Mario: Sticker Star | 2.49 million[3] | November 11, 2012 | Role-playing | Intelligent Systems | Nintendo |
| 30 | Fire Emblem Awakening | 2.37 million[3] | April 19, 2012 | Tactical role-playing | Intelligent SystemsNintendo SPD | Nintendo |
| 31 | Yo-kai Watch Blasters: Red Cat Corps and White Dog Squad | 2.37 million[3] | July 11, 2015 | Role-playing | Level-5 | JP: Level-5WW: Nintendo |
| 32 | Yo-kai Watch 3 | 2.21 million[3] | July 16, 2016 | Role-playing | Level-5 | JP: Level-5WW: Nintendo |
| 33 | Yoshi's New Island | 2.06 million[3] | March 14, 2014 | Platform | Arzest | Nintendo |
| 34 | Lego City Undercover: The Chase Begins | 2.04 million[6] | April 21, 2013 | Action-adventure | TT Fusion | Nintendo |
| 35 | Monster Hunter XX | 1.80 million[7] | March 18, 2017 | Action role-playing | Capcom | Capcom |
| 36 | Dragon Quest XI: Echoes of an Elusive Age | 1.74 million[8] | July 29, 2017 | Role-playing | Square Enix | Square Enix |
| 37 | Pokémon Super Mystery Dungeon | 1.67 million[3] | September 17, 2015 | Roguelike | Spike Chunsoft | The Pokémon CompanyNintendo |
| 38 | Kirby: Planet Robobot | 1.64 million[3] | April 28, 2016 | Actionplatform | HAL Laboratory | Nintendo |
| 39 | Dragon Quest VII: Fragments of the Forgotten Past | 1.60 million[3] | February 7, 2013 | Role-playing | HeartbeatArtePiazza | JP: Square EnixWW: Nintendo |
| 40 | Mario Tennis Open | 1.58 million[5] | May 20, 2012 | Sports | Camelot Software Planning | Nintendo |
| 41 | Puzzle & Dragons Z: Pazudora Z | 1.50 million[9] | December 12, 2013 | Puzzle | GungHo Online Entertainment | JP: GungHo Online EntertainmentWW: Nintendo |
| 42 | Pokémon Red / Green / Blue / Yellow[b] | 1.50 million[10] | February 27, 2016 | Role-playing | Game Freak | Nintendo |
| 43 | Professor Layton and the Miracle Mask | 1.48 million[3] | February 26, 2011 | Puzzleadventure | Level-5 | JP: Level-5WW: Nintendo |
| 44 | Style Savvy: Trendsetters | 1.44 million[3] | September 27, 2012 | Simulation | Syn Sophia | Nintendo |
| 45 | Pokémon Rumble Blast | 1.40 million[3] | August 11, 2011 | Action role-playingbeat 'em up | Ambrella | The Pokémon CompanyNintendo |
| 46 | Bravely Default | 1.40 million[3] | October 11, 2012 | Role-playing | Silicon Studio | Nintendo |
| 47 | Pokémon Mystery Dungeon: Gates to Infinity | 1.38 million[6] | November 23, 2012 | Roguelike | Spike Chunsoft | The Pokémon CompanyNintendo |
| 48 | Kid Icarus: Uprising | 1.37 million[3] | March 22, 2012 | Third-person shootershoot 'em up | Project SoraSora Ltd. | Nintendo |
| 49 | The Legend of Zelda: Tri Force Heroes | 1.36 million[3] | October 22, 2015 | Action-adventure | Nintendo EPDGrezzo | Nintendo |
| 50 | Super Street Fighter IV: 3D Edition | 1.30 million[4] | February 26, 2011 | Fighting | DimpsCapcom | Capcom |
| 51 | Kingdom Hearts 3D: Dream Drop Distance | 1.30 million[3] | March 29, 2012 | Action role-playing | Square Enix | Square Enix |
| 52 | Miitopia | 1.22 million[3] | December 8, 2016 | Role-playing | Nintendo EPD | Nintendo |
| 53 | Fantasy Life | 1.11 million[3] | December 27, 2012 | Role-playing | Level-5 | JP: Level-5WW: Nintendo |
| 54 | Mario & Luigi: Paper Jam | 1.08 million[5] | December 3, 2015 | Role-playing | AlphaDream | Nintendo |
| 55 | Star Fox 64 3D | 1.07 million[3] | July 14, 2011 | Rail shooter | Nintendo EADQ-Games | Nintendo |
| 56 | Rhythm Heaven Megamix | 1.03 million[3] | June 11, 2015 | Rhythm | Nintendo SPD | Nintendo |
| 57 | Monster Strike | 1 million[11] | December 17, 2015 | Role-playing | Mixi | Xflag |
| 58 | Style Savvy: Fashion Forward | 1 million[5] | April 16, 2015 | Simulation | Syn Sophia | Nintendo |
| 59 | Fire Emblem Echoes: Shadows of Valentia | 1 million[3] | April 20, 2017 | Tactical role-playing | Intelligent Systems | Nintendo |
| 60 | None | None | None | None | None | None |
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