The Southern Fleurieu was initially inhabited primarily by the Kaurna people who openly communicated with the Ramindjeri people, based at Encounter Bay. Aboriginal history credits the land forms of the Southern Fleurieu to the travels of Tjilbruke as he grieved carrying the body of his nephew from the Sturt River to Cape Jervis.

The Southern Fleurieu Peninsula was first mapped by Europeans in 1802 with both Nicholas Baudin and Matthew Flinders travelling the coastline. The French explorer Baudin named the Fleurieu Peninsula.

Rapid Bay was the first landing on the mainland by William Light in 1836 who declared the area "rich beyond expectation". The glowing report resulted in the early intensive settlement of the area.

The District was considered for the site of the new settlement of South Australia, before further surveying revealed the suitability of the present location of Adelaide.

Governor Hindmarsh recorded the aboriginal pronunciation of "Yoongalilla", as applied to the District and noted this in dispatches of 1837.

Both the French and British names for geographical features persisted in early mapping until the 1911 visit by the Count of Fleurieu to Adelaide. The visit resulted in recommendations for the present naming being made to the Royal Geographical Society of Australia.

Sealers and whalers are credited as being the first Europeans to establish semi-permanent habitation on the Fleurieu Peninsula and on Kangaroo Island in the early 1800s. A whaling station was built at Fishery Beach, near Cape Jervis and operated in the mid 1840s. The station was closed in 1855 after ships were lost at sea, the number of whales declined and petroleum oil became commercially available.

Evidence of Mega-fauna, in the form of bones attributed to Diprotodon, Maesopus - a giant kangaroo and Thylacoleo - a marsupial lion, were unearthed in the 1890s. A Diprotodon leg bone was found in a swamp in the 1890s and conjecture surrounds the possibility that the animals were hunted by local aboriginal groups.

Farming land in the District was surveyed for purchase in 1838. Land was released in 1840 and communities were established at Myponga, Second Valley, Rapid Bay and later at Yankalilla. Sheep, potatoes and wheat were quickly in production. Beans, flax, tobacco, oats, maize and barley were grown widely. Flour milling was established at Second Valley, Normanville and Yankalilla and jetties were constructed to handle the produce to local shipping. Mining, timber milling and tannin production from wattle bark became successful local industries in the mid 1800s. Dairying became a major rural industry from the 1840s onwards to the present day. Butter and cheese were exported early in the District's history.

In 1852 the South Australian Government proclaimed an Act of Parliament appointing District Councils to administer local affairs. The District Council of Yankalilla was constituted on 5th April, 1854.