The county was formed April 1, 1840, from Mackinac County. It was first named Tonedagana County and renamed Emmet County on March 8, 1843. Emmet County remained attached to Mackinac County for administrative purposes until county government was organized in 1853. The county was named for the Irish patriot Robert Emmet, who was hanged as a traitor to the British government at the age of 23. Sixteen counties were renamed in 1843 and five were given names of Irish origin, supposedly in deference to the increasing presence of settlers in Michigan with an Irish background. See List of Michigan county name etymologies.
Emmet County is located at the top of the mitten-shaped Lower Peninsula of Michigan, with Lake Michigan to the west, the Straits of Mackinac to the north, Cheboygan County to the east, and Charlevoix County to the south.
Emmet County is home to Michigan's most endangered species and one of the most endangered species in the world: the Hungerford's Crawling Water Beetle. The species lives in only five locations in the world, two of which are in Emmet County. One of these, a two and a half mile stretch downstream from the Douglas Road crossing of the East Branch of the Maple River supports the only stable population of the Hungerford's Crawling Water Beetle, with roughly 1000 specimens. This area is largely within and along the boundary of the University of Michigan Biological Station there. The other location in Emmet County, near the Oliver Road crossing of the Carp Lake River, revealed 4 adult specimens in 1997, but erosion at the road seems to have harmed the habitat and no specimens were found in the last survey conducted in 2003.
Ottawa history records that Emmet County was thickly populated by a race of Indians that they called the Mush-co-desh, which means, "the Prairie tribe." The Mush-co-desh had an agrarian society and were said to have "shaped the land by making the woodland into prairie as they abandoned their old worn out gardens which formed grassy plains". Ottawa tradition claims that they slaughtered from forty to fifty thousand Mush-co-desh and drove the rest from the land after the Mush-co-desh insulted an Ottawa war party.
When European explorers and settlers first arrived in the area it became part of New France, Ottawa and Ojibwe Indians were the principal inhabitants. The French established Fort Michilimackinac in about 1715. The British took the fort in 1761 and continued to use it as a trading post. In 1763, Ojibwe Indians took the fort as a part of Pontiac's Rebellion and held it for a year before the British retook it. The British abandoned the wooden fort in 1781 after building the limestone Fort Mackinac on nearby Mackinac Island. An Indian community on the lakeshore in the western part of the county continued to thrive after the British abandoned the fort.
In the 1840s, Indian villages lined the Lake Michigan shore from present-day Harbor Springs to Cross Village. The area was mostly reserved for native tribes by treaty provisions with the U.S. federal government until 1875.
In 1847, a group of Mormons settled on nearby Beaver Island and established a "kingdom" led by "King" James Jesse Strang. There were bitter disputes between Strang's followers and other white settlers. Strang, seeking to strengthen his position became a member of the Michigan State House of Representatives. In January 1853, he pushed through legislation titled, "An act to organize the County of Emmet", which enlarged Emmet County by attaching the nearby Lake Michigan islands to the county as well as a portion of Cheboygan County. Further, it attached the old Charlevoix County, which was originally named Keskkauko County and was as yet still unorganized, as a township of Emmet County. Due to Strang's influence, Mormons came to dominate county government, causing an exodus of many non-Mormon settlers to neighboring areas. In 1855, the non-Mormon resistance succeeded in getting the Michigan Legislature to reorganize the County of Emmet with the islands, including Beaver Island and North and South Manitou Island, set off into the separate Manitou County, which effectively eliminated Mormons from Emmet County government.
On April 27, 1857 an election selected Little Traverse (now named Harbor Springs) as the county seat. However, at about this time, a group of investors were trying to promote development at Mackinaw City and due to their influence, in February 1858, the State Legislature passed an act establishing Mackinaw City as the county seat. The Emmet County Board of Supervisors protested that the county seat had already been established at Little Traverse, and in 1861, the act was repealed as unconstitutional. In a contested election in 1867, residents voted to move the county seat to Charlevoix, which was upheld by a Circuit Court decision in 1868. However, in 1869, Charlevoix County was split off from Emmet County and its county seat was now in another county. No provisions for official relocation were authorized, although Harbor Springs served as the unofficial county seat until April 1902, when the present county seat of Petoskey was selected in a county-wide election.
Charlevoix Township was organized in 1853 and included all ot the nine townships presently in the southern half of the county. In the 1855 reorganization, four new townships were created by the State Legislature:
In 1855, county supervisors also established Arbour Croche Township and Utopia Township. The state had inadvertently drawn boundaries for Little Traverse and Bear Creek that such that one area was included in both. The county supervisors Arbour Croche was defined as having the same boundaries as the state-defined Little Traverse Township, excluding the area overlapping with Bear Creek. Eventually the name Arbour Croche disappeared in favor of Little Traverse. The township of Utopia was later absorbed into other townships.
In 1877, six additional townships were organized:
Center Township was added in 1878 and Carp Lake Township in 1879. Resort Township and Springvale Township, Michigan were formed in 1880, but were at that time part of Charlevoix County. Those townships, along with Bear Creek, experienced numerous boundary changes. The now defunct townships of Bear Lake and Spring Lake were created out of portions of these townships. In 1897, the portions of these townships remaining in Emmet County were absorbed into Bear Creek and Springvale Townships.
Also organized in 1897 were West Traverse Township (from portions of Friendship and Little Traverse Townships) and Egleston Township (name changed to McKinley Township in 1903). In 1923, Wawatam Township was the last township organized in the county, when it was detached from Carp Lake Township.