Hadashi no Gen is based on the events experienced by author Keiji Nakazawa and other survivors of Hiroshima. After publishing the one-shot Ore wa Mita, Nakazawa's editor encouraged him to write more of his experiences. The manga was first serialized in Shonen Jump in 1973, but was cancelled the following year due to low polling. It continued publication in three different magazines until concluding in 1987—Shimin (Citizen), Bunka Hyouron (Cultural Criticism), and Kyouiku Hyouron (Educational Criticism). Nakazawa planned to write a sequel following Gen becoming a mangaka in Tokyo, but this idea was scrapped when he retired due to failing eyesight and illness.

Hadashi no Gen was first published in English as Gen of Hiroshima in comic book format by EduComics, in cooperation with the pacifist organization Project Gen, a group of voluntary translators that sought to bring the manga to a larger audience. Volunteers around the world likewise picked up this project, partially translating this title into French, Italian, German, Portuguese, Swedish, Finnish, Norwegian, Indonesian, Tagalog, Esperanto, and by 1994, completely into Russian.

In English, only two comic book issues were released originally between January 1980 and April 1981 before the publication was cancelled. Since then, a number of publishers partially published the series as Barefoot Gen, including New Society Publishers, who published the first four volumes from September 3, 1986 to December 1, 1993; Penguin Books, who published the first two volumes from August 1, 1989 to August 1, 1990, under the Penguin Originals imprint, with a new edition published July 27, 1995; and Last Gasp, who started publication from September, 1986, initially only publishing the first four volumes. After the revival of Project Gen, Last Gasp finally published all ten volumes unabridged (with subtitles) from September 1, 2004 to February 1, 2010.