Flagstone was named by the Minister for Natural Resources on 24 April 1997 as a neighbourhood within districts of Undullah and Jimboomba. It was gazetted as a suburb within the City of Logan on 20 May 2016.
Flagstone as a suburb had started to form by 1996, with the development of the streets off Bushman Drive. The area to the south of Flagstone State School adjacent to Sandy Gully, as well as the school itself, were developed by 2001. The bulk of the development to the west of the Sydney Brisbane railway line occurred after 2011.
Flagstone Community College opened in 2002.