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In the parish of South Colah, Pennant Hills is one of the oldest settled areas of Hornsby Shire.
The original inhabitants of the area were Dharug people.
The first European settlers in the district acquired land at Carlingford, and David Kilpack, a convict who arrived in the colony in 1788 on the First Fleet, held the first land grant within the Hornsby Shire boundaries. 
There are a number of possibilities given for the naming of the suburb, though it is generally believed that Pennant Hills is named after the English botanist Thomas Pennant, who was a friend of Sir Joseph Banks. Some historians argued however that the name originated because of a signalling post stationed on a hill in the region, where flags were raised to signal when the governor was travelling from Sydney to Parramatta. The area was also referred to as Pendant Hills or Pennant Hills as early as 1800. At this time, Pennant Hills included the suburb of Ermington on the Parramatta River.
The earliest landholders in the district included a number of South Sea missionaries as well as the Reverend Samuel Marsden and Dr Thomas Arndell, who in 1799 had adjoining properties of 100 acres (40 hectares) each, near the present day Thompsons Corner.
Pennant Hills started out as a lumber camp for convicts on the western side of what is now the intersection of Pennant Hills and Hull roads.
Governor Macquarie, on a tour of the colony, was so impressed by the huge trees growing in the Pennant Hills region that he organised convicts under the supervision of Patrick Kelly, the superintendent carpenter, to start logging the forests. They set up a camp in 1816 and began felling the tall trees, mostly blue gum, blackbutt, forest oak and cedar.  The camp was augmented in 1819 by moving the centre of activity three kilometres along the ridge to Epping.
By 1830 most of the best timber had been cut, and timber getting gave way to the establishment of farms and orchards.
In 1856 James Bellamy purchased the land grant of Senior Constable John Thorn, who gave Thornleigh its name. The property of 723 acres (293 hectares) was divided among his children and mostly put to fruit-growing. Another of the early settlers was Joseph Henry Shields, who also bought a section of Thorn's grant for a citrus and summer fruit orchard. 
The orchards at Pennant Hills in the 1860s and 1870s were famous throughout the colonies for the high quality and huge quantities of fruit produced.
Pennant Hills railway station was opened on 5 April 1887, and was built for the people living at what is now West Pennant Hills. Although there was already a siding at Thornleigh, Pennant Hills residents asked for an additional siding to be built for the loading of produce grown from farms as far away as Dural. A goods siding was opened in 1898,  and became so popular that at the height of its use orchardists would queue six days a week to unload their fruit and collect empty crates. Because of the short time it took to convey fruit to Sydney from Pennant Hills by rail, orchardists started growing soft fruits such as nectarines, peaches, plums and other stone fruit, which would have spoilt over the long haul by road.
The coming of the railway, with four trains a day, and the fruit growers bringing their produce to the sidings, meant an increase in business. Eaton's hotel was built, servicing not only the local population, but travellers and holidaymakers from Sydney. In addition, there were a number of businesses such as a blacksmith, farrier and a wheelwright.
A trig station was established in 1889 on the corner of Pennant Hills and Beecroft roads. An observatory called Red Hill was built there in the 1890s,  and the observations made were of great importance at the time.
The principal wireless station for the whole of Australia was situated at Pennant Hills from 1912. It was 122 metres high. The site later became the Sydney Transmission Centre for Amalgamated Wireless Australasia Limited. The wireless mast has since been demolished.
 Hornsby Shire Historical Society, Pioneers of Hornsby Shire 1788-1901, Library of Australian History, Sydney, 1979, p 64
 Hornsby Shire Historical Society, Pioneers of Hornsby Shire 1788-1901, Library of Australian History, Sydney, 1979, p 74
 Hornsby Shire Council Works Department, Historical Notes by GL Ross, Hornsby Shire Council, Hornsby, New South Wales, 1966
 Patricia Dewey, 'Coming of the railway to the Hornsby', Local Colour, vol 6, p 5
 RC Taylor, Pennant Hills Public School 1925–1975, KTR Printing, Croydon, New South Wales, 1975