Stephen Murphy-Shigematsu has two families: one hailing from Ireland and the other from Japan. His paternal ancestors emigrated from southwestern Ireland to the northeastern United States near the end of the 19th century. His grandmother died when his father was still a child, leaving her eldest daughter to raise the kids.

On his mother's side, Murphy-Shigematsu's great-grandfather was a hatamoto, a samurai in direct service to the shogun. His great-grandfather changed his name from Yamamoto to Shigematsu after fleeing the 1868 battle of Ueno during the Boshin War. He fled to the town of Matsuyama where he was protected by friendly samurai.

Murphy-Shigematsu's parents met after World War II. Both worked in the building that served as SCAP General Headquarters, she as a translator.