Between 1840 and 1841, surveyors William Austin Burt, John Mullett and Charles W. Cathcart, surveyed much of Northern Michigan. Cathcart oversaw the internal lines survey for 34N 08W, the region which would later be known as Charlevoix. Mullett and Cathcart laid out many of the townships in the new county including Charlevoix Township.
The county was named in 1843 for Pierre François Xavier de Charlevoix, a Jesuit missionary of the French colonial era. The county was originally organized in 1840 as Kesk-kauko in honor of a great chief of the Saginaw tribe, and name was changed from Resh-kanko to Charlevoix County in 1843.
In 1847, a group of "Strangite" Mormons settled on 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, gained election to 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 Emmet county, as well as a portion of Cheboygan County and Keskkauko/Resh-kanko/ Charlevoix. Charlevoix was thus organized in 1853 as a township under Emmet County and consisted all of the nine townships in the southern half of Emmet County.
Due to Strang's influence, Mormons came to dominate Emmet 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 Emmet County. The islands, including Beaver Island and North and South Manitou Islands, were transferred into the separate Manitou County, which effectively eliminated Mormons from Emmet County government. After an assassination attempt on June 20, 1856, Strang died three weeks later.
Emmet County continued to experience tensions as citizens clashed over whether to put the county seat at Little Traverse (Harbor Springs) versus Mackinaw City. 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 from Emmet County, resulting in Charlevoix being the official county seat for Emmet county as well as for the newly formed Charlevoix County.