Kojima directs and writes Policenauts, a cinematic adventure game with influences from cyberpunk and hard science fiction. It's released for the PC-9821 in Japan and later ported to other platforms.

Kojima produces Boktai: The Sun Is in Your Hand, a unique action RPG for the Game Boy Advance that utilizes a solar sensor on the cartridge. The game's gameplay is heavily reliant on exposure to sunlight.

Kojima produces Metal Gear Acid, a turn-based tactical card game set in the Metal Gear universe, for the PSP.

Kojima produces Metal Gear Acid 2, a sequel to Metal Gear Acid for the PSP, improving on its mechanics and art style.

Kojima Productions assists with the development of Castlevania: Lords of Shadow. Kojima serves as a producer on the project, providing guidance and creative input. MercurySteam developed the game.

Kojima has been involved with the Zone of the Enders series in various capacities, primarily as producer. He supported its anime-esque mecha action style.