Prior to European settlement, Aboriginal people of the Bibbulmun tribe inhabited the Boyup Brook Shire. Boyup Brook got its name from the Aboriginal word “Booyup”, which means “Place of Big Stones” or “Place of Big Smoke”. Either one fits as Booyup is the name of the big pool on the brook a few kilometres from the townsite. This pool is surrounded by a thick stand of  grass trees and the smoke from these when burnt would create a “Big Smoke”. The Big Stones” would refer to the large granite outcrops which are common in the area. The town was established where the brook runs into the river.

The discovery of the area is credited to the explorer Augustus Gregory, Assistant Surveyor, who in 1845 conducted a survey mission, travelling from the upper reaches of the Blackwood River, where the Arthur and Beaufort Rivers converged, and followed the river for 171 kilometres. He carved his initials and the date on a large Jarrah Tree. The tree is now dead, but his marks are still on the stump, which has now been covered for preservation.

The first settlers arrived in 1854, when a Commodore Scott and his wife took up a 12,000 acre lease. The first enterprise was dairying and the family produced butter and cheese which was transported to Albany. Later, wool production took over as the main source of income.

In 1861, James George Lee Steere, his wife Caroline and a Mr J Monger took up a 100,000 acre grazing lease. Ten years later, in 1871 came William Forrest, brother of Lord Forrest.

By 1882 there were nineteen families here and in 1900 a school was built - the beginning of a town. In 1909 the railway from Donnybrook was completed as far as Boyup Brook and in 1911 was extended towards Kojonup. The early settlers etched out a living by kangaroo hunting, and timber cutting. Although sandalwood mainly grew in the Kojonup/Williams area, many of the early pioneers were involved in the industry as well as carting the product by horse and dray to Bunbury, as the old sandalwood track went through the McAlinden area.

Boyup Brook was declared a town site on February 9, 1900 and a school was constructed in the same year. After the railway from Donnybrook was extended to reach Boyup Brook town site in 1909, Boyup Brook became the commercial and administrative centre for the district.

Mr. P.D. Forrest was a local pioneer in the development of Western Australia’s subterranean clover industry, developing “Dwalganup” clover and clover harvesting machinery between 1910 and the Second World War.

A number of timber mills began operating in the district prior to the Second World War with large timber mills at Boyup Brook (closed 1982) and Wilga, and smaller ones in the out lying districts.

The cultivation and processing of flax was also carried out in Boyup Brook. During World War II, the flax was required for war materials such as tarpaulins, webbing and parachute harnesses. The Flax Mill, which was opened in 1941, was the only mill to continue to operate after the war, closing in 1965.