Human habitation in the Baton Rouge area has been dated to
12000 – 6500 BC, based on evidence found along the Mississippi,
Earthwork mounds were built by hunter-gatherer societies in the
Middle Archaic period, from roughly the 4th millennium BC.
 The Proto-
Muskogean language divided into its descendant languages by about 1000 BC; a cultural boundary between either side of
Mobile Bay and the
Black Warrior River began to appear between about 1200 BC and 500 BC, a period called the Middle "Gulf Formational Stage". The Eastern Muskogean language began to diversify internally in the first half of the 1st millennium AD.
The early Muskogean societies were the bearers of the
Mississippian culture, which formed around AD 800 and extended in a vast network across the Mississippi and Ohio valleys, with numerous
chiefdoms in the Southeast as well. By the time the
Spanish made their first forays inland from the shores of the
Gulf of Mexico in the early 16th century, by some evidence many political centers of the Mississippians were already in decline, or abandoned. At the time, the region appeared to be occupied by a collection of moderately-sized native chiefdoms interspersed with autonomous villages and tribal groups.
 There is, however, also evidence that these societies were thriving at the time of the first Spanish contact, and that later Spanish expeditions encountered the aftermath of the diseases spread unknowingly by the first expedition.
Pierre Le Moyne, Sieur d'Iberville, named Baton Rouge and lakes
in the early French colonial era.
Pierre Le Moyne d'Iberville led an exploration party up the
Mississippi River in 1699. The explorers saw a red pole marking the boundary between the
Bayogoula tribal hunting grounds. The French name le bâton rouge ("the red stick") is the translation of a native term rendered as Istrouma, possibly a corruption of the
Choctaw iti humma ("red pole");
 André-Joseph Pénicaut, a carpenter traveling with d'Iberville, published the first full-length account of the expedition in 1723. According to Pénicaut,
From there [
Manchacq] we went five leagues higher and found very high banks called écorts in that region, and in savage called Istrouma which means red stick [bâton rouge], as at this place there is a post painted red that the savages have sunk there to mark the land line between the two nations, namely: the land of the Bayagoulas which they were leaving and the land of another nation—thirty leagues upstream from the baton rouge—named the Oumas.
Red Sticks for the ceremonial use of red sticks among the
The location of the red pole was presumably at Scott's Bluff, on what is now the campus of
 It was reportedly a 30-foot-high (9.1 m) painted pole adorned with fish bones.
The settlement of Baton Rouge by Europeans began in 1721 when a military post was established by French colonists. Since European settlement, Baton Rouge has been governed by France, Britain, Spain, Louisiana, the
Republic of West Florida, the
Confederate States, and the United States. In 1755, when French-speaking settlers of
Acadia in Canada's
Maritime provinces were
driven into exile by British forces, many took up residence in rural Louisiana. Popularly known as
Cajuns, the descendants of the Acadians maintained a separate culture. During the first half of the 19th century, the city grew steadily as the result of
steamboat trade and transportation.
Baton Rouge was
incorporated in 1817. In 1822, the
Pentagon Barracks complex of buildings was completed. The site has been used by the Spanish, French, British, Confederate States Army, and United States Army and was part of the short-lived Republic of West Florida.
 In 1951, ownership of the barracks was transferred to the State of Louisiana, and in 1976 it was placed on the National Register of Historic Places.
In 1846, the state legislature designated Baton Rouge Louisiana's new capital to replace "sinful"
New Orleans. The architect
James Dakin was hired to design the Capitol building in Baton Rouge, with construction beginning in late 1847.
 Rather than mimic the federal
Capitol in Washington, as many other states had done, he designed a capitol in
Neo-Gothic, complete with turrets and crenellations, and stained glass, which overlooks the Mississippi. It has been described as the "most distinguished example of Gothic Revival" architecture in the state and has been designated as a
National Historic Landmark.
Map of Baton Rouge in 1863
By the outbreak of the
Civil War, the population of Baton Rouge was nearly 5,500. The war nearly halted economic progress, except for businesses associated with supplying the
Union Army occupation of the city beginning in the spring of 1862. The
Confederates at first consolidated their forces elsewhere, during which time the state government was moved to
Opelousas and later
 In the summer of 1862, about 2,600 Confederate troops under generals
John C. Breckinridge (the former
Vice President of the United States) and
Daniel Ruggles tried in vain to recapture Baton Rouge.
After the war, New Orleans served as the seat of the
Reconstruction Era state government. When the
Bourbon Democrats regained power in 1882, they returned the state government to Baton Rouge, where it has since remained. In his 1893 guidebook, Karl Baedeker described Baton Rouge as "the Capital of Louisiana, a quaint old place with 10,378 inhabitants, on a bluff above the Mississippi".
In the 1950s and 1960s, Baton Rouge experienced a boom in the
petrochemical industry, causing the city to expand away from the original center.
A building boom that began in the 1990s continued into the 2000s, during which Baton Rouge was one of the fastest-growing cities in the
South in terms of technology,
 and Metropolitan Baton Rouge was one of the fastest growing metropolitan areas in the U.S. (under 1 million), with 602,894 in 2000 and 802,484 people as of the 2010 census.
 Baton Rouge's population temporarily surged after
Hurricane Katrina (2005), as it accepted as many as 200,000 displaced residents.
July 5, 2016 saw the
shooting of Alton Sterling, a black man, by police officers.
 This was followed by civil rights protests and unrest. On July 17, Gavin Eugene Long
shot six police officers resulting in three deaths.
 The Baton Rouge Metropolitan area was affected by the
2016 Louisiana floods in August.