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The first people to live in the area that became Cowan were the Guringai Aboriginal people.
There is some debate regarding the origins of the suburb's name, which was referred to in 1826 on applications for land grants. The word Cowan is possibly a Guringai word first recorded in the area in 1823, but the meaning is not known. Alternatively, Cowan is also believed by some to be an Aboriginal word meaning 'big water', 'opposite' or 'the other side'. Another suggestion is that the name related to a tree carved with the word Cowa, an Aboriginal word for mountain. 
The 1828 census lists two convicts called Cowan,  and it is also thought possible that Cowan was named after one of them. Still another suggestion is that it was named after a small town in Scotland.
Besides the botanist George Caley, who explored the area in 1805, the first Europeans to visit the area were timber-getters. The timber from Cowan was used for coach building, one of the first industries in the area. 
The railway stop at Cowan was originally a crossing loop to allow trains on the single-line north track to pass each other, and it was also the point at which auxiliary steam engines, connected to the trains at Hawkesbury River station (Brooklyn), were disconnected after the steep haul to the top of the plateau.  A station and platform was constructed in 1901.
With the coming of the railway, Cowan become a popular holiday spot and a regular starting point for bushwalkers.
In 1958, the rail line was electrified, and this also increased the number of people visiting the area, with families moving into the suburb, particularly those wanting to raise children in a bushland setting but near the city.
There has been little change in Cowan village since it was first laid out as a crown subdivision in 1910. Lots ranged from 1,500 to 4,500 square metres.
The population of Cowan has remained relatively static since 1966, when there were 500 people, increasing to 522 in 1991 and rising only to 549 in 2001.
The predominance of freestanding three-bedroom houses set in gardens provides a sense of openness, and creates a pleasant transition to the bushland which surrounds the town.
 Norma Olliff, There must be a river: The history of the Shire of Hornsby, the author, Sydney, 1973
 Hornsby Shire Historical Society, 'The origin of Berowra and Cowan', Local Colour, vol 4 no 11, p 7
 Frances Pollen, The book of Sydney Suburbs, Angus & Robertson, Sydney, 1988, p 72
 Pat Dewey, Local Colour, vol 6, no 8