Prior to the arrival of European settlers, the Pinjarra area was inhabited for thousands of years by the Bindjareb Bilyidar (river) Nyungars. In 1830 (following the establishment of the Swan River Colony in 1829) Thomas Peel was granted a substantial area of land (250,000 acres) from Cockburn Sound to the Murray River .
The area, now known as the Peel Region, intended for farming use, as all of the fertile lands near the Swan River Settlement had already been taken up. Included in the Murray region was Pinjarra and in 1831 land for the townsite was reserved. 
Unfortunately, the town did not get off to a very good start.
The conflict between the new settlers and the Nyungars slowly increased as tribal lands near the river were taken up by the farmers. Cattle were speared and so too some settlers. The area became a treacherous and dangerous place to be. Apart from stock and both settlers and Aborigines being killed or speared, some crops and buildings were also destroyed (mainly by fire). As unrest continued an incident involving the death of a servant Hugh Nesbit brought the conflict between settlers and Aboriginals to ahead. 
Stirling, along with John Septimus Roe, Captain Ellis and a detachment of soldiers headed to the banks of the Murray River to confront the Bindjareb Bilyidar Nyungars.
On October 28th, 1834, they surrounded the Nyungars and opened fire on them. The Battle of Pinjarra, otherwise known as the Pinjarra Massacre, would go down in Western Australian history as one of the State’s darkest and bloodiest days.
Ironically, in the following years, the farming families in Pinjarra praised the vital role the Bindjareb Nyungars played in the community following the massacre. Together they worked in clearing land and working the farms.
In 1836 Lieutenant Bunbury sent a detachment of soldiers to be stationed at the new town of Pinjarra. The following year it was allocated for settlers. In the 1840s the first of five bridges was built over the Murray River, even though transport via the river was still the most popular mode of transport. In 1865 the town was surveyed and 6 years later the Murray Roads Board was established. Pinjarra was shown on earlier maps as either Pinjarrup or Pinjarrah however in 1880 the townsite was gazetted as Pinjarra.