42 titles- Blue City (Tokyo: Sōbisha, 1976)
- Harukanaru Asa ["Faraway Morning"] (Tokyo: Shūeisha, 1977)
- Kyojintachi no Densetsu ["Legend of the Titans"] (Tokyo: Shūeisha, 1978)
- Umi no Ha ["Fangs of the Sea"] (Tokyo: Sōbisha, 1979)
- Saber Tiger (Tokyo: Shūeisha, 1981)
- Yōsei Densetsu ["Legends of the Enchantress/Siren"] (Tokyo: Shūeisha, 1981)
- Sanzō ["An Afterimage"] (Tokyo: Shūeisha, 1982)
- Yamato no Hi ["Fires of Yamato"] (Tokyo: Shūeisha, 1984)
- 2001-ya Monogatari ["Tales of 2001 Nights"] (Tokyo: Shūeisha, 1985)
- Star Field (Tokyo: Futabasha, 1986)
- Yamataika (Tokyo: Ushio Shuppan-sha, 1987)
- Saber Tiger (Tokyo: Shūeisha, 1987)
- 2001 Nights (San Francisco, California: Viz Communications, 1987)
- Blue City (Tokyo: Shūeisha, 1988)
- Kyojintachi no Densetsu ["Legend of the Giants"] (Tokyo: Shūeisha, 1988)
- Harukanaru Asa ["Faraway Morning"] (Tokyo: Shūeisha, 1988)
- Ivan Dejavu no Ichinichi ["One Day in the Life of Ivan Dejavu"] (Tokyo: Sōbisha, 1988)
- Ōinaru Kaisen ["The Broadening Horizon"] (Tokyo: Shinshokan, 1988)
- Bem Hunter Sword (Tokyo: Kōdansha, 1991)
- Saber Tiger (San Francisco, California: Viz Communications, 1991)
- Blue Hole (Tokyo: Kōdansha, 1992)
- Megacross (Tokyo: Ushio Shuppan-sha, 1992)
- Mirai no Futatsu no Kau ["The Two Faces of the Future"] (Tokyo: Kōdansha, 1993) with James P Hogan
- Stardust Memories (Tokyo: Scholar, 1995)
- Munakata Kyōju Denkikō ["The Strange Investigations of Professor Munakata"] (Tokyo: Ushio Shuppan-sha, 1996)
- Blue World (Tokyo: Kōdansha, 1996)
- Chronicle (Tokyo: Asahi Sonorama, 1996)
- Midway Rekishi-hen ["Midway: History"] (Tokyo: Shūeisha, 2000)
- Midway Uchū-hen ["Midway: Space"] (Tokyo: Shūeisha, 2001)
- Kodoku Experiment ["Isolation Experiment"] (Tokyo: Gentōsha, 2003)
- El Alamein no Shinden ["Temple of El Alamein"] (Tokyo: Gentōsha, 2003)
- Moon Lost (Tokyo: Kodansha, 2004)
- Horobishi Kemonotachi no Umi ["Monsters Beneath the Sea"] (Tokyo: Gentōsha, 2004)
- Kamunabi ["Divine Southern Fires"] (Tokyo: Shūeisha, 2004)
- Munakata Kyōju Ikōroku ["The Case Records of Professor Munakata"] (Tokyo: Ushio Shuppan-sha, 2005-ongoing)
- The Two Faces of Tomorrow (Milwaukie, OR: Dark Horse Comics, 2006)
- Pilots: Shoki Ga Shūsei ["Pilots: Collected Early Works"] (Tokyo: Chikuma, 2006)
- Hoshino Yukinobu SF Sakuhin Shūsei III ["Collected SF of Yukinobu Hoshino"] (Tokyo Kōbunsha, 2008)
- Hoshino Yukinobu SF Sakuhin Shūsei I: Continent ["Collected SF of Yukinobu Hoshino"] (Tokyo Kōbunsha, 2008)
- Hoshino Yukinobu SF Sakuhin Shūsei 2: Space ["Collected SF of Yukinobu Hoshino"] (Tokyo Kōbunsha, 2008)
- Professor Munakata's British Museum Adventure (London: British Museum Press, 2011)
- Rain Man (Tokyo: Shōgakukan, 2015)