| Title | Developer | Publisher | Release dates |
| Anchorz Field | Sammy Corporation | Sammy Corporation | |
| Armored Unit | Sammy Corporation | Sammy Corporation | |
| Bakusou Dekotora Densetsu for WonderSwan | KID | Kaga Tech | |
| Beatmania for WonderSwan | Konami | Konami | |
| Buffers Evolution | Koto Laboratory | Bandai | |
| Cardcaptor Sakura: Sakura to Fushigi na Clow Card | SIMS Co., Ltd. | Bandai | |
| Chaos Gear ~Michibika reshi mono~ | | Bandai | |
| Chocobo no Fushigi na Dungeon for WonderSwan | TOSE | Bandai | |
| Chō Aniki: Otoko No Tamafuda | CP.BRAiN | Bandai | |
| Chou Denki Card Battle "Yōfu Makai" Kikuchi Hideyuki | Kobunsha | Kobunsha | |
| Clock Tower for WonderSwan | | Kaga Tech | |
| Crazy Climber | Nihon Bussan | Nihon Bussan | |
| Densha de Go! | Taito | Taito | |
| Densha de Go! 2 | Taito | Cyber Front | |
| Digimon Adventure: Anode Tamer | SIMS Co., Ltd. | Bandai | |
| Digimon Adventure: Cathode Tamer | | Bandai | |
| Digimon Adventure 02: Tag Tamers | SIMS Co., Ltd. | Bandai | |
| Digital Monster Ver.WonderSwan | SIMS Co., Ltd. | Bandai | |
| Digital Partner | | Bandai | |
| Dokodemo Hamster | Beck | Beck | |
| D's Garage21 Kōbo Game: Tane o maku tori | Avit, Inc. | Bandai | |
| Engacho! for WonderSwan | Nihon Application | Nihon Application | |
| Fever Sankyo Koushiki Pachinko Simulation for WonderSwan | Beck | Beck | |
| Final Lap 2000 | Soft Machine | Bandai | |
| Fire Pro Wrestling for WonderSwan | S-Plan Corporation | Kaga Tech | |
| Fishing Freaks: Bass Rise for Wonder Swan | | Beck | |
| From the TV Animation:One Piece ~Mezase Kaizokuou!~ | Soft Machine | Bandai | |
| Ganso JaJaMaru-kun | Jaleco | Jaleco | |
| Glocal Hexcite | Success | Success | |
| Gomokunarabe & Reversi Tōryūmon | Sammy Corporation | Sammy Corporation | |
| Gorakuou Tango! | | Mobius | |
| Gunpey | Koto Laboratory | Bandai | |
| Hanafuda Shiyouyo | | Success | |
| Harobots | | Sunrise Interactive | |
| Hunter × Hunter: Ishi o Tsugu Mono | Yoshidayama-Workshop Co., Ltd | Bandai | |
| Kakutō Ryōri Densetsu: Bistro Recipe -Wonder Battle Hen- | Banpresto | Banpresto | |
| Kaze no Klonoa: Moonlight Museum | Namco | Bandai | |
| Keiba Yosō Shien Soft: Yosō Shinkaron | Beck | Beck | |
| Kiss Yori... -Seaside Serenade- | KID | KID | |
| Kosodate Quiz Dokodemo My Angel | | Bandai | |
| Kyousouba Ikusei Simulation: Keiba | Beck | Beck | |
| Langrisser Millennium WS: The Last Century | CP.BRAiN | Bandai | |
| Last Stand | Soft Machine | Bandai | |
| Lode Runner for WonderSwan | Aisystem Tokyo | Banpresto | |
| Macross: True Love Song | Lay-Up | Lay-Up | |
| Magical Drop for WonderSwan | Gai Brain Y K | Data East | |
| Mahjong Tōryūmon | | Sammy Corporation | |
| Makaimura for WonderSwan | Team OX | Bandai | |
| Medarot Perfect Edition (Kabuto Version) | | Imagineer | |
| Medarot Perfect Edition (Kuwagata Version) | | Imagineer | |
| Meitantei Conan: Majutsushi No Chousenjou | Tomcat System | Bandai | |
| Meitantei Conan: Nishi No Meitantei Saidai No Kiki!? | Tomcat System | Bandai | |
| Metakomi Therapy: Nee Kiite! | Media Entertainment | Media Entertainment | |
| Mingle Magnet | HAL Corporation | HAL Corporation | |
| Mobile Suit Gundam MSVS | | Bandai | |
| Moero!! Pro Yakyuu Rookies | TOSE | Jaleco | |
| Morita Shogi for WonderSwan | Yuki Enterprise | Yuki Enterprise | |
| Nazo-Oh Pocket | Avit, Inc. | Bandai | |
| Neon Genesis Evangelion: Shito Ikusei | Gainax | Bandai | |
| Nice On | Aisystem Tokyo | Sammy Corporation | |
| Nihon Pro Mahjong Renmei Kōnin Tetsuman | Chat Noir / Naxart | Kaga Tech | |
| Nobunaga no Yabō for WonderSwan | Koei | Koei | |
| O-Chan no Oekaki Logic | Santaclaus | Sunsoft | |
| Pocket Fighter | Soft Machine | Bandai | |
| Pro Mahjong Kyoku for WonderSwan | Athena | Athena | |
| Puyo Puyo 2 | Compile | Bandai | |
| Puzzle Bobble | Yoshidayama-Workshop Co., Ltd | Sunsoft | |
| Rainbow Islands: Putty's Party | Digitalware | Megahouse | |
| Ring: Infinity | Kadokawa Shoten | Kadokawa Shoten | |
| Robot Works | | Bandai | |
| Rockman & Forte Mirai kara no Chōsensha | Layup Co., Ltd. | Bandai | |
| Sangokushi for WonderSwan | | Koei | |
| Sangokushi II | Koei | Koei | |
| SD Gundam: Emotional Jam | | Bandai | |
| SD Gundam: Gashapon Senki -Episode One- | Graphic Research Co., Ltd | Bandai | |
| SD Gundam: G Generation Gather Beat | Banpresto | Banpresto | |
| Senkaiden: TV Animation Senkaiden Houshin Engi Yori | Graphic Research Co., Ltd | Bandai | |
| Sen-Know Millennium | Kouyousha Ltd | Bandai | |
| Shanghai Pocket | | Sunsoft | |
| Shin Nihon Pro Wrestling: Tōkon Retsuden | TOSE | Tomy | |
| Shōgi Tōryūmon | Sammy Corporation | Sammy Corporation | |
| Side Pocket for WonderSwan | Data East | Data East | |
| Slither Link | Tomcat System | Bandai | |
| Soccer Yarou!: Challenge the World | | Coconuts Japan | |
| Sotsugyō for WonderSwan | | Bandai | |
| Space Invaders | | Sunsoft | |
| Super Robot Taisen Compact | TOSE | Banpresto | |
| Super Robot Taisen Compact 2 Dai1bu: Chijō Hadō Hen | TOSE | Banpresto | |
| Super Robot Taisen Compact 2 Dai2bu: Uchuu Gekishin Hen | TOSE | Banpresto | |
| Super Robot Taisen Compact 2 Dai3bu: Ginga Kessen-hen | TOSE | Banpresto | |
| Taikyoku Igo Heisei Kiin | Success | Success | |
| Tanjo: Debut for WonderSwan | | Bandai | |
| Tarepanda no Gunpey | Koto Laboratory | Bandai | |
| Tekken Card Challenge | Namco | Bandai | |
| Terrors | | Bandai | |
| Tetsujin 28-go | Megahouse | Megahouse | |
| Time Bokan Series: Bokan Densetsu: Buta mo Odaterya Doronboo | Alpha Unit | Banpresto | |
| Tokyo Majin Gakuen: Fuju Hōroku | | Asmik Ace | |
| Trump Collection: Bottom Up Teki Trump Seikatsu | Bottom Up | Bottom Up | |
| Trump Collection 2: Bottom Up Teki Sekai Isshuu no Tabi | Bottom Up | Bottom Up | |
| Turntablist: DJ Battle | Vestax | Bandai | |
| Umitsuri ni ikou! | | Coconuts Japan | |
| Uzumaki: Denshi Kaiki Hen | Omega Micott | Omega Micott | |
| Uzumaki: Noroi Simulation | Omega Micott | Omega Micott | |
| Vaitz Blade | | Bandai | |
| Wasabi Produce - Street Dancer | | Bandai | |
| Wonder Stadium | TOSE | Bandai | |
| Wonder Stadium '99 | Namco | Bandai | |
| WonderSwan Handy Sonar | | Bandai | |