At the beginning of recorded history, the Chicago area was inhabited by a number of Algonquian peoples, including the Mascoutens and Miamis. Trade links and seasonal hunting migrations linked these peoples with their neighbours, the Potawatomis to the east, Fox to the north, and the Illinois to the southwest. The name "Chicago" is the French version of the Miami-Illinois word shikaakwa ("wild leek"/"skunk"), named for the plants common along the Chicago River, and thus has nothing to do with Chief Chicagou of the Michigamea people.

Chicago's location at a short, swampy portage between the Chicago River (flowing originally into the Great Lakes) and the Des Plaines River (flowing into the Mississippi), attracted the attention of many French explorers travelling in the area, such as Louis Jolliet and Henri Joutel, who felt that the area had a great potential as a transportation hub. In 1683, French Jesuits built the Mission of the Guardian Angel to Christianize the local Wea and Miami people, and for a time there was a French fort (Fort Chécagou), commanded by Pierre de Liette. French and allied use of the Chicago portage was mostly abandoned during the 1720s thanks to continual raiding during the Fox Wars.

During the mid 1700s, the Chicago area was inhabited primarily by Potawatomis, who took the place of the Miami and Sauk and Fox who had previously controlled the area.

The first non-native settler in Chicago was Jean Baptiste Pointe du Sable, a Haitian of African descent, who settled on the Chicago River in the 1770s and married a local Potawatomi woman. In 1795, following the Northwest Indian War, the area of Chicago was ceded by the Native Americans in the Treaty of Greenville to the United States for a military post. In 1803, Fort Dearborn was built and remained in use until 1837, except between 1812 and 1816 when it was destroyed in the Fort Dearborn massacre during the War of 1812. The Ottawa, Ojibwa, and Potawatomi ceded the land to the United States in the 1816 Treaty of St. Louis.

On August 12, 1833, the Town of Chicago was incorporated with a population of 350. The first boundaries of the new town were Kinzie, Desplaines, Madison, and State Streets, which included an area of about three-eighths of a square mile (1 km²).

Within seven years the town had a population of over 4,000. Chicago was granted a city charter by the State of Illinois on March 4, 1837. The opening of the Illinois and Michigan Canal in 1848 allowed shipping from the Great Lakes through Chicago to the Mississippi River and the Gulf of Mexico. The first rail line to Chicago, the Galena & Chicago Union Railroad was completed the same year. Chicago would go on to become the transportation hub of the United States with its road, rail, water and later air connections. Chicago also became home to national retailers offering catalog shopping using these connections like Montgomery Ward and Sears, Roebuck and Company.

Due to the geography of Chicago, early citizens faced many problems. The prairie bog nature of the area provided a fertile ground for disease-carrying insects. Early on, Chicago's population and commerce growth was stymied by lack of good transportation infrastructure, though this problem was soon remedied. During spring Chicago was so muddy from the high water that horses would be stuck past their legs in the street. One dirt road was so hazardous that it became known as the "Slough of Despond." Comical signs proclaiming "Fastest route to China" or "No Bottom Here" were placed out to warn people of the mud.

To address these transportation problems, the board of Cook County commissioners, decided to improve two country roads toward the West and Southwest. The first road went west, crossing the "dismal Nine-mile Swamp," crossed the Des Plaines River, and went southwest to Walker's Grove, now known as Plainfield. There is a dispute about the route of the second road to the South.

Early Chicago was also plagued by sewer and water problems. Many people described it as the filthiest city in America. To solve this problem Chicago embarked on the creation of a massive sewer system. In the first phase sewage pipes were laid across the city above ground with gravity moving the waste. The city was built in a low-lying area subject to flooding. In 1856 the city council decided that the entire city should be elevated four to five feet using a newly available jacking-up process. Most of the houses were at that time built of wood, making the task easier. In one remarkable instance the 5-story Brigg’s Hotel weighing 22,000 tons was lifted while it continued to operate. Observing that such a thing could never have happened in Europe, British Historian Paul Johnson cites this astounding feat as a dramatic example of American determination and ingenuity based on the conviction that anything material is possible.

In 1840, Chicago was the ninety-second most populous city in the United States. Its population grew so rapidly that twenty years later, it was the ninth most populous city in the country. Thirty years after that it had grown to become the nation's second largest city, and one of the largest cities in the world. By 1857 Chicago was the largest city in what was then known as the Northwest. In a period of twenty years Chicago grew from 4,000 people to over 90,000.

The 1860 Republican National Convention in Chicago nominated home-state candidate Abraham Lincoln.

During the election of April 23, 1875, the voters of Chicago choose to operate under the Illinois Cities and Villages Act of 1872. Chicago still operates under this act, in lieu of a charter. The Cities and Villages Act has been revised several times since, and may be found in Chapter 65 of the Illinois Compiled Statutes.

In 1871, most of the city burned in the Great Chicago Fire. The damage from the fire was immense; 300 people died, 18,000 buildings were destroyed and nearly 100,000 of the city's 300,000 residents were left homeless. One of the factors contributing to the fire's spread was the abundance of wood; the streets, sidewalks and many buildings were built of wood. The fire led to the incorporation of stringent fire-safety codes that included a strong preference for masonry construction. Unfortunately, the soft, swampy ground near the lake proved unstable ground for tall masonry buildings, a situation which led directly to the use of steel frames and the invention in Chicago of the skyscraper.

While at the time the fire damage was devastating, history has shown that it proved to be a benefit to the city and surrounding communities. City planners had wanted to implement a radical redesign of the city in a Beaux Arts tradition yet politics and infighting stalled these plans as developers and citizens began immediate reconstruction on the existing Jeffersonian grid. The building boom that followed saved the city's status as the transportation and trade hub of the Midwest. Massive reconstruction using the newest materials and methods catapulted Chicago into its status as a city on par with New York and established the city as the birthplace of modern architecture in the United States.

Other notable fires occurred in Chicago. 602 persons died in the Iroquois Theater fire in 1903. The LaSalle Hotel fire in 1946 claimed the lives of 61 guests. On December 1, 1958, the Our Lady of the Angels School Fire occurred at the Roman Catholic elementary school, Our Lady of the Angels School in the Humboldt Park area of Chicago. The fire occurred 18 minutes before the end of the school day, killed 92 students and 3 nuns and led to fire safety improvements to public and private schools in the United States.

The deeply polarized attitudes of labor and business classes in Chicago prompted a strike by workers lobbying for an eight-hour work day. A peaceful demonstration on May 4, 1886, at Haymarket near the west side was interrupted by a bomb thrown at police; seven police officers died. A group of anarchists were tried for inciting the riot and convicted; several were hanged and others were pardoned. The episode weakened the labor movement as it acquired a reputation for violence.

Between 1870 and 1900 Chicago grew from a city of 299,000 to nearly 1.7 million, the fastest-growing city in human history at the time. Chicago's flourishing economy brought huge numbers of new residents from rural communities and immigrants from Europe. The growth in Chicago's manufacturing and retail sectors came to dominate the Midwest and greatly influence the nation's economy. The Chicago Union Stock Yards dominated the packing trade. Chicago became the world's largest rail hub, and one of its busiest ports.

The constant lobbying by the city's boasting lobbyists and politicians earned Chicago the nickname "Windy City" in the New York press, although this etymology may be erroneous. The city adopted the nickname as its own.

The Exposition was constructed on former marshland at the present location of Jackson Park along Lake Michigan in Chicago's Hyde Park neighborhood. The land was reclaimed according to a design by landscape architect Frederick Law Olmsted and the pavilions, which followed a classical theme, were designed by committee of the city's architects under the direction of Daniel Burnham.

The World's Columbian Exposition drew 27.5 million visitors, and is considered among the most influential world's fairs in history, with a wide ranging impact in art, architecture and design. The fair also featured the first, and until recently, largest Ferris Wheel ever built.

Lake Michigan — the primary source of fresh water for the city — was already highly polluted from the rapidly growing industries in and around Chicago; a new way of procuring clean water was needed. The city embarked on a large tunnel excavation project and began building tunnels below Lake Michigan to newly built water cribs. The water cribs were two miles (three kilometers) off the shore of Lake Michigan. The cribs failed to bring enough clean water because spring rains would wash the polluted water from the Chicago River into them. Beginning in 1855, Chicago constructed the nations' first comprehensive sewer system in the U.S. Chicago's water and sewage systems were publicly managed, a model soon followed by other cities. In 1900 the problem of sewage was solved by reversing the direction of the River's flow with the construction of the Chicago Sanitary and Ship Canal leading to the Illinois River.

The 1920s brought international notoriety to Chicago as gangsters, such as Al Capone, battled each other and the law during the Prohibition era. Nevertheless, this decade also saw a large increase in industry in the city as well as the first arrivals of the Great Migration that would lead thousands of mostly Southern blacks to Chicago and other Northern cities. New construction occurred rapidly, with notable Chicago landmarks such as the Merchandise Mart and art deco Chicago Board of Trade Building completed in 1930.

On December 2, 1942, the world's first controlled nuclear reaction was conducted at the University of Chicago as part of the top secret Manhattan Project.

Starting in the 1950s, many upper- and middle-class citizens left the inner-city of Chicago for the suburbs, and the city itself shrank by nearly 700,000, leaving many impoverished neighborhoods in their wake. Since the early 1990s, Chicago has seen a turnaround from the decline common to American cities following World War II. Many formerly abandoned neighborhoods are starting to show new life and the city's diversity has grown with larger percentages of ethnic groups such as Asians, Mexicans and Puerto Ricans. In the 1990s alone, Chicago gained 113,000 new inhabitants. Since the 1920s the lakefront has been crowded with high rise apartment buildings for middle classes who work in the city (few of them have children, however). (The lakefront is warmer in winter and cooler in summer.) Many decaying inner-city neighborhoods on the North and West sides have been gentrified by young couples.

Mayor Richard J. Daley was elected in 1955, in the era of so-called machine politics. During Daley's tenure (he died in office in 1976), the violence-filled 1968 Democratic National Convention was held in Chicago, four major expressways were built, the Sears Tower became the world's tallest building and O'Hare Airport (which became the world's busiest airport) was constructed. Major riots burned out sections of the black neighborhoods of the South and West side, especially in 1968.

In 1979 Jane Byrne, the city's first woman mayor, was elected, winning the Democratic primary by mobilizing a black protest vote. In 1983, Harold Washington became the first black mayor of Chicago. Richard M. Daley, son of Richard J. Daley, became mayor in 1989, and has been repeatedly reelected.

One new development under the younger Daley has sparked debate, the destruction of the city's vast public housing projects. New projects during Daley's administration have been making world headlines and have made Chicago larger, environmentally friendlier, and more accessible. With a new skyline to form in 2009, the city is growing faster with a denser atmosphere and a more breathable one as well. The park district, which is committed to the biodiversity recovery plan, is set to restore damaged natural areas of the city as well as creating new ones, including the creation of rooftop gardens on most flattop skyscrapers.