The county was named for Andrew Jackson, a General of the War of 1812, who had served as Florida's first military governor for six months in 1821.

The following year the county court met at "Chipola Settlement", which is also known as Waddell's Mill Pond.

Cotton was cultivated as a commodity crop by large workgangs, and so Florida became a slave society.

They enticed the Florida Legislature with offers of free land, locally paying for construction of a county courthouse and development of a related public square, and donating an additional $500 to purchase a quarter section of land to be sold at public auction as a way to finance the new government, if the county seat was moved to Marianna.

Webbville's prominent citizens moved to Marianna to follow the courts, as did numerous businesses.

When the L&N Railroad decided to bypass putting a station at Webbville, the town declined further and became defunct.

[citation needed] After the Civil War, the county was convulsed by violence as Confederate veterans and their allies attacked and intimidated freedmen and their sympathizers.

The county faced the worst economic conditions in the state, as it had been most extensively developed for cotton plantations before the war, and was adversely affected by the international decline in the market.

[8]: 462  In addition the two representatives of the Freedmen's Bureau, Charles Memorial Hamilton and William J. Purman, worked to break the cycle of black labor exploitation.

Planters would throw sharecroppers off the land at the end of the season with no payment, claiming infractions that the Bureau deemed minor.

The local Ku Klux Klan, insurgent Confederate Army veterans, directed their violence at eradicating the Republican Party in the county, assassinating more than 150 Republican Party leaders and other prominent African Americans as part of a successful campaign to retain white Democratic power in the county.

[9] Another source says that in Jackson County, 200 "leading Republicans" were assassinated in 1869 and 1870 alone; no one was arrested or brought to trial for these crimes.

The last Republican official in the county, clerk of the circuit court John Dickenson, was assassinated in 1871.

)[8]: 552 In testimony to Congressional hearings about the KKK, state senator Charles H. Pearce, minister of the African Methodist Episcopal Church, said, "Satan has his seat; he reigns in Jackson County.

In 1934, Claude Neal, an African-American suspect in the murder of a young white woman, was tortured, shot and hanged in a spectacle lynching that was announced beforehand on the radio and in a local paper.

Howard Kester, a prominent Southern evangelical minister who tried to improve conditions, assessed the economic and class issues related to the racial violence.

Blue Springs is a Jackson county recreation area east of Marianna located near the site of former Florida Governor John Milton's Sylvania plantation.

Two other notable water bodies in the county are Compass Lake in the southwest and Ocheesee Pond in the southeast.

The 2020 United States census counted 47,319 people, 17,083 households, and 11,179 families in Jackson County, Florida.

[21] The 2016-2020 5-year American Community Survey estimates show that the median household income was $40,754 (with a margin of error of +/- $1,741).

The last time a Democrat won the county in the presidential election was 1980, when Jimmy Carter, the former governor of neighboring Georgia, was on the ballot.

The county is part of Florida's 2nd congressional district, represented by Neal Dunn (R-Panama City).

[36] The Florida Department of Juvenile Justice Dozier School for Boys, closed in 2011 after extensive investigations of abuse, was located in Marianna.

In 2018, the department fired deputy Zachary Wester, who was arrested for planting drugs in the vehicles of innocent motorists.

The primary one is the CSX P&A Subdivision, a line formerly owned by the Louisville and Nashville Railroad that served Amtrak's Sunset Limited.

Other lines within the county were abandoned after restructuring of the railroad industry in the mid to late 20th century.