The first settlers of the area were Muscogee-speaking people. The Chickasaw traditionally claim to have settled around 1300 after coming east across the Mississippi. A combination of factors, including disease, land disputes between the Choctaw and Cherokee, and pressures from the United States government had largely depopulated the area by the time Revolutionary War veteran John Hunt settled in the land around the Big Spring in 1805. The 1805 Treaty with the Chickasaws and the Cherokee Treaty of Washington of 1806 ceded native claims to the United States government. The area was subsequently purchased by LeRoy Pope, who named the area Twickenham after the home village of his distant kinsman Alexander Pope.

Twickenham was carefully planned, with streets laid out on the northeast to southwest direction based on the flow of Big Spring. However, due to anti-British sentiment during this period, the name was changed to "Huntsville" to honor John Hunt, who had been forced to move to other land south of the new city.

Both John Hunt and LeRoy Pope were Freemasons and charter members of Helion Lodge #1, the oldest Lodge in Alabama.

In 1811, Huntsville became the first incorporated town in Alabama. However, the recognized "founding" year of the city is 1805, the year of John Hunt's arrival. The city celebrated its sesquicentennial in 1955 and its bicentennial in 2005.

David Wade arrived in Huntsville in 1817. He built the David Wade House on the north side of what is now Bob Wade Lane (Robert B. Wade was David's grandson) just east of Mt. Lebanon Road. It had six rough Doric columns on the portico.

During the Great Depression, the Wade House was measured as part of the Historic American Buildings Survey (HABS) to be included in the government's Archive and was photographed by Frances Benjamin Johnston for the project. This project put architects, draftsmen, and photographers to work to create an inventory of documentation and photographs of significant properties across the country. The house had already been abandoned for years and was considerably deteriorated. It was torn down in 1952. Today only the antebellum smokehouse, an imposing structure itself, survives at the property.

Huntsville's quick growth was from wealth generated by the cotton and railroad industries. Many wealthy planters moved into the area from Virginia, Georgia, and the Carolinas.^{[citation needed]} In 1819, Huntsville hosted a constitutional convention in Walker Allen's large cabinet making shop. The 44 delegates meeting there wrote a constitution for the new state of Alabama. In accordance with the new state constitution, Huntsville became Alabama's first capital when the state was admitted to the Union. This was a temporary designation for one legislative session only. The capital was moved to more central cities; to Cahawba, then to Tuscaloosa, and finally to Montgomery.

In 1855, the Memphis and Charleston Railroad was constructed through Huntsville, becoming the first railway to link the Atlantic seacoast with the lower Mississippi River.

Huntsville initially opposed secession from the Union in 1861, but provided many men for the Confederacy's efforts. The 4th Alabama Infantry Regiment, led by Col. Egbert J. Jones of Huntsville, distinguished itself at the Battle of Manassas/Bull Run, the first major encounter of the American Civil War. The Fourth Alabama Infantry, which contained two Huntsville companies, were the first Alabama troops to fight in the war and were present when Lee surrendered to Grant at Appomattox Court House in April 1865. Nine generals of the war were born in or near Huntsville, split five to the Confederate and four to the Union.

On the morning of April 11, 1862, Union troops led by General Ormsby M. Mitchel seized Huntsville in order to sever the Confederacy's rail communications and gain access to the Memphis & Charleston Railroad. Huntsville was the control point for the Western Division of the Memphis & Charleston, and by controlling this railroad the Union had struck a major blow to the Confederacy.

During the first occupation, Union officers occupied many of the larger homes in the city while the enlisted soldiers camped mainly on the outskirts. In the initial occupation, the Union troops searched for both Confederate troops hiding in the town and weapons. Since they occupied the city, treatment toward Huntsville was relatively civil. However, residents of the nearby towns did not fare as well.

The Union troops were forced to retreat only a few months later, but they returned to Huntsville in the fall of 1863 and thereafter used the city as a base of operations for the war, except during the last months of 1864. While many homes and villages in the surrounding countryside were burned in retaliation for the active guerrilla warfare in the area, Huntsville itself survived because it housed Union Army troops.

After the Civil War, Huntsville became a center for cotton textile mills, such as Lincoln, Dallas, and Merrimack. Each mill company constructed worker housing, in communities that included schools, churches, grocery stores, theaters, and hardware stores, all within walking distance of the mill. In some of these, workers were required to buy goods at the company stores, which sometimes overcharged them. The mill owners could throw out workers from housing if they violated policies about behavior.^{[citation needed]}

A dairy cow called Lily Flagg broke the world record for butter production in 1892. Her Huntsville-resident owner General Samuel H. Moore painted his house butter yellow and organized a party to celebrate, arranging for electric lights for the dance floor. An area south of Huntsville was named Lily Flagg before 1906. This area was later annexed by the city.

During the 1930s, industry declined in Huntsville due to the Great Depression. Huntsville became known as the Watercress Capital of the World because of its abundant harvest in the area. Madison County led Alabama in cotton production during this time.

By 1940, Huntsville was still relatively small, with a population of about 13,000 inhabitants. This quickly changed in early 1941 when the U.S. Army selected 35,000 acres (140 km²) of land adjoining the southwest area of the city for building three chemical munitions facilities: the Huntsville Arsenal, the Redstone Ordnance Plant (soon redesignated Redstone Arsenal), and the Gulf Chemical Warfare Depot. These operated throughout World War II, with combined personnel approaching 20,000. Resources in the area were strained as new workers flocked to the area, and the construction of housing could not keep up.

At the end of the war in 1945, the munitions facilities were no longer needed. They were combined with the designation Redstone Arsenal (RSA), and a considerable political and business effort was made in attempts to attract new tenants. One significant start involved manufacturing the Keller automobile, but this closed after 18 vehicles were built. With the encouragement of US Senator John Sparkman, the U.S. Army Air Force considered this for a major testing facility, but then selected another site. Redstone Arsenal was prepared for disposal, but Sparkman used his considerable Southern Democratic influence (the Solid South controlled numerous powerful chairmanships of congressional committees) to persuade the Army to choose it as a site for rocket and missile development.

In 1950, about 1,000 personnel were transferred from Fort Bliss, Texas, to Redstone Arsenal to form the Ordnance Guided Missile Center (OGMC). Central to this was a group of about 200 German scientists and engineers, led by Wernher von Braun; they had been brought to America by Colonel Holger Toftoy under Operation Paperclip following World War II. Assigned to the center at Huntsville, they settled and reared families in this area.

As the Korean War started, the OGMC was given the mission to develop what eventually became the Redstone Rocket. This rocket set the stage for the United States' space program, as well as major Army missile programs, to be centered in Huntsville. Toftoy, then a brigadier general, commanded OGMC and the overall Redstone Arsenal. In early 1956, the Army Ballistic Missile Agency (ABMA) under Major General John Medaris was formed.

The city is nicknamed "The Rocket City" for its close association with U.S. space missions. On January 31, 1958, ABMA placed America's first satellite, Explorer 1, into orbit using a Jupiter-C launch vehicle, a descendant of the Redstone. This brought national attention to Redstone Arsenal and Huntsville, with widespread recognition of this being a major center for high technology.^{[citation needed]}

On July 1, 1960, 4,670 civilian employees, associated buildings and equipment, and 1,840 acres (7.4 km²) of land, transferred from ABMA to form NASA's George C. Marshall Space Flight Center (MSFC). Wernher von Braun was MSFC's initial director. On September 8, President Dwight D. Eisenhower formally dedicated the MSFC.

During the 1960s, the major mission of MSFC was in developing the Saturn boosters used by NASA in the Apollo Lunar Landing Program. For this, MSFC greatly increased its employees, and many new companies joined the Huntsville industrial community. The Cummings Research Park was developed just north of Redstone Arsenal to partially accommodate this industrial growth, and has now become the second-largest research park of this type in America.

Huntsville's economy was nearly crippled and growth almost came to a standstill in the 1970s following the closure of the Apollo program. However, the emergence of the Space Shuttle, the International Space Station, and a wide variety of advanced research in space sciences led to a resurgence in NASA-related activities that has continued into the 21st century. In addition, new Army organizations have emerged at Redstone Arsenal, particularly in the ever-expanding field of missile defense.

Now in the 2000s, Huntsville has the second-largest technology and research park in the nation, and ranks among the top 25 most educated cities in the nation. It is considered in the top of the nation's high-tech hotspots, and one of the best Southern cities for defense jobs. It is the number one United States location for engineers most satisfied with the recognition they receive, with high average salary and low median gross rent.

More than 25 biotechnology firms have developed in Huntsville due to the Huntsville Biotech Initiative. The HudsonAlpha Institute for Biotechnology is the centerpiece of the 150-acre Cummings Research Park Biotech Campus, part of the 4,000-acre Cummings Research Park, which is second only to North Carolina's Research Triangle Park in land area. The non-profit HudsonAlpha Institute has contributed genomics and genetics work to the Encyclopedia of DNA Elements (ENCODE). For-profit business ventures within the Biotech Campus focus on subjects such as infectious disease diagnostics, immune responses to disease and cancer, protein crystallization, lab-on-a-chip technologies, and improved agricultural technologies. The University of Alabama in Huntsville (UAH) created a doctoral program in biotechnology to help develop scientists to support HudsonAlpha in addition to the emerging biotechnology economy in Huntsville. The university's strategic plan has biotechnology as one of its emerging fields for future education and research.

As of the 2010 census, there were 180,105 people, 77,033 households, and 45,416 families residing in the city. The population density was 861.5 people per square mile (332.7/km²). There were 84,949 housing units at an average housing density of 405.3 per square mile (156.9/km²). The racial makeup of the city was 61.3% White, 30.7% Black or African American, 0.4% Native American, 2.6% Asian, 0.1% Pacific Islander, 2.9% from other races, and 2.8% from two or more races. Hispanic or Latino of any race were 6.2% of the population.

There were 77,033 households, out of which 24.9% had children living with them, 40.1% were married couples living together, 14.5% had a female householder with no husband present, and 41.0% were non-families. 34.7% of all households were made up of individuals, and 10.2% had someone living alone who was 65 years of age or older. The average household size was 2.25 and the average family size was 2.91.

As of the 2000 census, there were 158,216 people, 66,742 households, and 41,713 families residing in the city. The population density was 909.0 people per square mile (351.0/km²). There were 73,670 housing units at an average density of 423.3 per square mile (163.4/km²). The racial makeup of the city was 64.47% White, 30.21% Black or African American, 0.54% Native American, 2.22% Asian, 0.06% Pacific Islander, 0.66% from other races, and 1.84% from two or more races. Hispanic or Latino of any race were 2.04% of the population. Non-Hispanic Whites were 58% of the population in 2010, compared to 86.9% in 1970.

There were 66,742 households, out of which 27.6% had children living with them, 45.5% were married couples living together, 13.7% had a female householder with no husband present, and 37.5% were non-families. 32.3% of all households were made up of individuals, and 9.2% had someone living alone who was 65 years of age or older. The average household size was 2.29 and the average family size was 2.91. Same-sex couple households comprised 0.5% of all households.