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Eiji Ōtsuka was born in the city formerly known as Tanashi, Tokyo (currently Nishitōkyō, Tokyo). His father, as a repatriate from Manchuria, suffered poor living conditions in repatriate housing prior to his acceptance into university. Ōtsuka's father was a member of the former Japanese Communist Party, but he left the party due to disagreements regarding party policy.

In middle school, Ōtsuka joined the dōjin circle Sakuga Group, which lead to his employment as an assistant for manga artist Tarō Minamoto in his first year at high school. The following year, Ōtsuka, with references from Minamoto, debuted as a gag manga artist. However, he soon ended his career as a manga artist during his college entrance exams after deciding that he lacked talent as a manga artist. Ōtsuka graduated the University of Tsukuba in March of 1981. There, he studied Japanese folkloristics under the guidance of professor Tokuji Chiba. Ōtsuka gave up the notion of attending graduate school after he was told by instructor Miyata Noboru that his "ideas are too journalistic and not suited for academics".

After graduation, Ōtsuka worked part-time as the editor of the magazines Ryuu and Petit Apple Pie, together with manga artist Yukio Sawada. As a part-time editor, he worked with manga artist Shoutarou Ishomori for about a month, where he learned how to parse manga names (a "name" refers to the rough draft of a manga page, with preliminary panel layout, dialogue and plot, which is commonly checked by an editor before the artist proceeds to the manuscript phase). Later shifting from part-time to full-time editor, Ōtsuka worked as the editor-in-chief of the manga magazine Manga Burikko on a freelance basis. The comments he published in the magazine under a pseudonym became the basis of Ōtsuka's later career as a commentator.

During his tenure at Manga Burikko, Ōtsuka was involved in the trial of a serial kidnapper and murderer of young girls, active between 1988 and 1989 in Saitama, Tokyo. The suspect (and later convicted perpetrator), Tsutomu Miyazaki, was found to have possessed a large collection of manga, which at the time meant that the manga subculture was "repeatedly" linked to Miyazaki in the press and in popular imagination, creating the image that "young people involved with amateur manga are dangerous, psychologically disturbed perverts." Ōtsuka contested this popular perception, later writing that he "became somewhat angry about how judgment of [Miyazaki's] crimes kept shifting onto otaku hobbies or tastes." It was also during this time that the first official use of the term "otaku" was published in Manga Burikko, with Ōtsuka still serving as its editor-in-chief.

Ōtsuka goes on to lecture at various Japanese universities and colleges on the topic of manga studies. In 2007, he receives his PhD from Kobe Design University, with the doctoral dissertation titled "From Mickey's format to Proposition of Atom : the origin of postwar manga methodology in wartime years and its development".