Waikonini may originally have been part of Peel Forest Station, which was taken up by Francis Jollie in 1853. Jollie died in 1870 and the run came into the possession of Edward Cooper. Cooper sold the run in 1878 to partnership Smith, Dennistoun, and Co.

During the 1860s, the Crown granted the land on which Waikonini sits to William Ashby. In 1879 the property was sold to Martin Griffin, who in turn sold it to William Barker. Barker was a son of the noted early photographer Dr Barker of Christchurch who arrived in Canterbury with the first settlers in December, 1850.

William Edward Barker (1858-1935) was born in Christchurch and educated at Christ's College, Christchurch, and Jesus College, Cambridge, where he studied medicine. During this time he met his first wife, Gertrude Pritchett who was studying at Girton. College. It is understood that she persuaded him to give up his medical studies .

Barker returned to New Zealand following his marriage in 1880, and purchased the 150 acres at Peel Forest that he called Waikonini the following year. The house was probably built in 1882, and may have been designed by Gertrude's father, J.P Pritchett, an architect of Darlington, England. Gertrude died in 1884, and William married her sister Lucy in 1887, with whom he had seven children. Barker took up fruit growing, and by 1903 was considered 'thoroughly successful'. 11 acres were in trees, and fruit was being sent around the South Island. The remainder of the property was running sheep and cattle. Barker was also a beekeeper. He is remembered for his interests in botany and geology and he founded the Mount Peel Floral and Horticultural Association.

The house and property were sold out of the family in 1936 following William's death. Today it sits on a block of 50 acres.