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Flagstone takes its name from the outcrops of flag rock in the creek beds of the area. To the local Indigenous people, Round Mountain – which is located within the Flagstone area – is considered a sacred place. It borders several tribal areas and was used as a meeting place. The mountain has been set aside as a cultural heritage site.

Early settlers made their living from timber getting, and in sawmills and gravel pits. Many old timber-getting tracks can still be seen in the higher, western parts of the suburb. The railway line that bisects Flagstone is the South Brisbane to Kyogle line, which was completed in 1930 and continues to Sydney.

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

The suburb is named after Flagstone Creek, which flows into the Logan River just south of Chadwick Drive in South Maclean.