The original manga was written and illustrated by Takako Shimura. Shimura originally planned to use a female high school student who wants to become a boy as the main character. However, she realized that a boy who wants to become a girl before entering into puberty would have many worries related to growing up, and changed the story accordingly.
Related to previous work of Shimura - Shikii no Junin. Shimura took the junior high school teacher Kentaro Kaneda from Shikii no Junin and inserted him into Wandering Son, where he teaches at Shuichi's junior high school.
The Japanese title, Horo Musuko, is a pun on Hoto Musuko, meaning "prodigal son".