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Before Europeans arrived, the New Haven area was the home of the Quinnipiac tribe of Native Americans, who lived in villages around the harbor and subsisted off local fisheries and the farming of maize. The area was briefly visited by Dutch explorer Adriaen Block in 1614. Dutch traders set up a small trading system of beaver pelts with the local inhabitants, but trade was sporadic and the Dutch did not settle permanently in the area.

In 1637 a small party of Puritans reconnoitered the New Haven harbor area and wintered over. In April 1638, the main party of five hundred Puritans who had left the Massachusetts Bay Colony under the leadership of Reverend John Davenport and London merchant Theophilus Eaton sailed into the harbor. It was their hope to set up a theological community with the government more closely linked to the church than that in Massachusetts, and to exploit the area's excellent potential as a port. The Quinnipiacs, who were under attack by neighboring Pequots, sold their land to the settlers in return for protection.

By 1640, "Quinnipiac's" theocratic government and nine-square grid plan were in place, and the town was renamed Newhaven, with 'haven' meaning harbor or port. (However, the area to the north remained Quinnipiac until 1678, when it was renamed Hamden.) The settlement became the headquarters of the New Haven Colony, distinct from the Connecticut Colony previously established to the north centering on Hartford. Reflecting its theocratic roots, the New Haven Colony forbid the establishment of other churches, whereas the Connecticut Colony permitted them.

Economic disaster struck Newhaven in 1646, when the town sent its first fully loaded ship of local goods back to England. It never reached its destination, and its disappearance stymied New Haven's development versus the rising trade powers of Boston and New Amsterdam.

In 1660, Colony founder John Davenport's wishes were fulfilled, and Hopkins School was founded in New Haven with money from the estate of Edward Hopkins.

In 1661, the Regicides who had signed the death warrant of Charles I of England were pursued by Charles II. Two of them, Colonel Edward Whalley and Colonel William Goffe, fled to New Haven for refuge. Davenport arranged for them to hide in the West Rock hills northwest of the town. Later a third judge, John Dixwell, joined the others.

In 1664 New Haven became part of the Connecticut Colony when the two colonies were merged under political pressure from England. Some members of the New Haven Colony seeking to establish a new theocracy elsewhere went on to establish Newark, New Jersey.

It was made co-capital of Connecticut in 1701, a status it retained until 1873.

In 1716, the Collegiate School relocated from Old Saybrook to New Haven, establishing New Haven as a center of learning. In 1718, in response to a large donation from East India Company merchant Elihu Yale, former Governor of Madras, the name of the Collegiate School was changed to Yale College.^{[citation needed]}

For over a century, New Haven citizens had fought in the colonial militia alongside regular British forces, as in the French and Indian War. As the American Revolution approached, General David Wooster and other influential residents hoped that the conflict with the government in Britain could be resolved short of rebellion. On 23 April 1775, which is still celebrated in New Haven as Powder House Day, the Second Company, Governor's Foot Guard, of New Haven entered the struggle against the British parliament. Under Captain Benedict Arnold, they broke into the powder house to arm themselves and began a three-day march to Cambridge, Massachusetts. Other New Haven militia members were on hand to escort George Washington from his overnight stay in New Haven on his way to Cambridge. Contemporary reports, from both sides, remark on the New Haven volunteers' professional military bearing, including uniforms.

On July 5, 1779, 2,600 loyalists and British regulars under General William Tryon, governor of New York, landed in New Haven Harbor and raided the 3,500-person town. A militia of Yale students had been preparing for battle, and former Yale president and Yale Divinity School professor Naphtali Daggett rode out to confront the Redcoats. Yale president Ezra Stiles recounted in his diary that while he moved furniture in anticipation of battle, he still couldn't quite believe the revolution had begun. New Haven was not torched as the invaders did with Danbury in 1777, or Fairfield and Norwalk a week after the New Haven raid, so many of the town's colonial features were preserved.

New Haven was incorporated as a city in 1784, and Roger Sherman, one of the signers of the Constitution and author of the "Connecticut Compromise", became the new city's first mayor.

The city struck fortune in the late 18th century with the inventions and industrial activity of Eli Whitney, a Yale graduate who remained in New Haven to develop the cotton gin and establish a gun-manufacturing factory in the northern part of the city near the Hamden town line. That area is still known as Whitneyville, and the main road through both towns is known as Whitney Avenue. The factory is now the Eli Whitney Museum, which has a particular emphasis on activities for children and exhibits pertaining to the A. C. Gilbert Company. His factory, along with that of Simeon North, and the lively clock-making and brass hardware sectors, contributed to making early Connecticut a powerful manufacturing economy; so many arms manufacturers sprang up that the state became known as "The Arsenal of America". It was in Whitney's gun-manufacturing plant that Samuel Colt invented the automatic revolver in 1836. Many other talented machinists and firearms designers would go on to found successful firearms manufacturing companies in New Haven, including Oliver Winchester and O.F. Mossberg & Sons.

The Farmington Canal, created in the early 19th century, was a short-lived transporter of goods into the interior regions of Connecticut and Massachusetts, and ran from New Haven to Northampton, Massachusetts.

New Haven was home to one of the important early events in the burgeoning anti-slavery movement when, in 1839, the trial of mutineering Mende tribesmen being transported as slaves on the Spanish slaveship Amistad was held in New Haven's United States District Court. There is a statue of Joseph Cinqué, the informal leader of the slaves, beside City Hall. See "Museums" below for more information. Abraham Lincoln delivered a speech on slavery in New Haven in 1860, shortly before he secured the Republican nomination for President.

The American Civil War boosted the local economy with wartime purchases of industrial goods, including that of the New Haven Arms Company, which would later become the Winchester Repeating Arms Company. (Winchester would continue to produce arms in New Haven until 2006, and many of the buildings that were a part of the Winchester plant are now a part of the Winchester Repeating Arms Company Historic District). After the war, population grew and doubled by the start of the 20th century, most notably due to the influx of immigrants from southern Europe, particularly Italy. Today, roughly half the populations of East Haven, West Haven, and North Haven are Italian-American. Jewish immigration to New Haven has left an enduring mark on the city. Westville was the center of Jewish life in New Haven, though today many have fanned out to suburban communities such as Woodbridge and Cheshire.

New Haven's expansion continued during the two World Wars, with most new inhabitants being African Americans from the American South and Puerto Ricans. The city reached its peak population after World War II. The area of New Haven is only 17 square miles (44 km²), encouraging further development of new housing after 1950 in adjacent, suburban towns. Moreover, as in other U.S. cities in the 1950s, New Haven began to suffer white flight of middle-class workers. One author suggested that aggressive redlining and rezoning made it difficult for residents to obtain financing for older, deteriorating urban housing stock, thereby condemning such structures to deterioration.^{[additional citation(s) needed]}

In 1954; then-mayor Richard C. Lee began some of the earliest major urban renewal projects in the United States. Certain sections of downtown New Haven were redeveloped to include museums, new office towers, a hotel, and large shopping complexes. Other parts of the city, particularly the Wooster Square and Fair Haven neighborhoods were affected by the construction of Interstate 95 along the Long Wharf section, Interstate 91, and the Oak Street Connector. The Oak Street Connector (Route 34), running between Interstate 95, downtown, and The Hill neighborhood, was originally intended as a highway to the city's western suburbs but was only completed as a highway to the downtown area, with the area to the west becoming a boulevard (See "Redevelopment" below).

In 1970, a series of criminal prosecutions against various members of the Black Panther Party took place in New Haven, inciting mass protests on the New Haven Green involving twelve thousand demonstrators and many well-known New Left political activists. (See "Political Culture" below for more information).

From the 1960s through the late 1990s, central areas of New Haven continued to decline both economically and in terms of population despite attempts to resurrect certain neighborhoods through renewal projects. In conjunction with its declining population, New Haven experienced a steep rise in its crime rate.

Since approximately 2000, many parts of downtown New Haven have been revitalized with new restaurants, nightlife, and small retail stores. In particular, the area surrounding the New Haven Green has experienced an influx of apartments and condominiums. In recent years, downtown retail options have increased with the opening of new stores such as Urban Oufitters, J Crew, Origins, American Apparel, Gant Clothing, and an Apple Store, joining older stores such as Barnes & Noble and Raggs Clothing. In addition, two new supermarkets opened to serve downtown's growing residential population. A Stop & Shop opened just west of downtown, while Elm City Market, located one block from the Green, opened in 2011. The recent turnaround of downtown New Haven has received positive press from various periodicals.

Major projects include the current construction of a new campus for Gateway Community College downtown, and also a 32-story, 500-unit apartment/retail building called 360 State Street. The 360 State Street project is now occupied and is the largest residential building in Connecticut. A new boathouse and dock is planned for New Haven Harbor, and the linear park Farmington Canal Trail is set to extend into downtown New Haven within the coming year. Additionally, foundation and ramp work to widen I-95 to create a new harbor crossing for New Haven, with an extradosed bridge to replace the 1950s-era Q Bridge, has begun. The city still hopes to redevelop the site of the New Haven Coliseum, which was demolished in 2007.

In April 2009, the United States Supreme Court agreed to hear a suit over reverse discrimination brought by 18 white firefighters against the city. The suit involved the 2003 promotion test for the New Haven Fire Department. After the tests were scored, no black firefighters scored high enough to qualify for consideration for promotion, so the city announced that no one would be promoted. In the subsequent Ricci v. DeStefano decision the court found 5-4 that New Haven's decision to ignore the test results violated Title VII of the Civil Rights Act of 1964. As a result, a district court subsequently ordered the city to promote 14 of the white firefighters.

In 2010 and 2011, state and federal funds were awarded to Connecticut (and Massachusetts) to construct the Hartford Line, with a southern terminus at New Haven's Union Station and a northern terminus at Springfield's Union Station. According to the White House, "This corridor has one train per day connecting communities in Connecticut and Massachusetts to the Northeast Corridor and Vermont. The vision for this corridor is to restore the alignment to its original route via the Knowledge Corridor in western Massachusetts, improving trip time and increasing the population base that can be served." Set for construction in 2013, the "Knowledge Corridor high speed intercity passenger rail" project will cost approximately $1 billion, and the ultimate northern terminus for the project is reported to be Montreal in Canada. Train speeds between will reportedly exceed 110 miles per hour (180 km/h) and increase both cities' rail traffic exponentially.

The U.S. Census Bureau reports a 2010 population of 129,779, with 47,094 households and 25,854 families within the city of New Haven. The population density was 6,859.8 people per square mile (2,648.6/km²). There were 52,941 housing units at an average density of 2,808.5 per square mile (1,084.4/km²). The racial makeup of the city was 42.6% White, 35.4% African American, 0.5% Native American, 4.6% Asian, 0.1% Pacific Islander, 12.9% from other races, and 3.9% from two or more races. Hispanic or Latino residents of any race were 27.4% of the population.Non-Hispanic Whites were 31.8% of the population in 2010, down from 69.6% in 1970. The city's demography is shifting rapidly: New Haven has always been a city of immigrants and the Latino population is growing rapidly. Previous influxes among ethnic groups have been African-Americans in the postwar era, and Irish, Italian and (to a lesser degree) Slavic peoples in the prewar period.

As of the 2010 census, of the 47,094 households, 29.3% had children under the age of 18 living with them, 27.5% include married couples living together, 22.9% had a female householder with no husband present, and 45.1% were non-families. 36.1% of all households were made up of individuals, and 10.5% had someone living alone who was 65 years of age or older. The average household size was 2.40 and the average family size 3.19.

The ages of New Haven's residents were 25.4% under the age of 18, 16.4% from 18 to 24, 31.2% from 25 to 44, 16.7% from 45 to 64, and 10.2% who were 65 years of age or older. The median age was 29 years, which was significantly lower than the national average. There were 91.8 males per 100 females. For every 100 females age 18 and over, there were 87.6 males.

The median income for a household in the city was $29,604, and the median income for a family was $35,950. Median income for males was $33,605, compared with $28,424 for females. The per capita income for the city was $16,393. About 20.5% of families and 24.4% of the population were living below the poverty line, including 32.2% of those under age 18 and 17.9% of those age 65 or over.

It is estimated that 14% of New Haven residents are pedestrian commuters, ranking it number four by highest percentage in the United States. This is primarily due to New Haven's small area and the presence of Yale University.

New Haven is noted for having the highest percentage of Italian American residents of any US city.

New Haven is a predominantly Roman Catholic city, as the city's Dominican, Irish, Italian, Mexican, Ecuadorian, and Puerto Rican populations are overwhelmingly Catholic. The city is part of the Archdiocese of Hartford. Jews also make up a considerable portion of the population, as do Black Baptists. There is a growing number of (mostly Puerto Rican) Pentecostals as well. There are churches for all major branches of Christianity within the city, multiple store-front churches, ministries (especially in working-class Latino and Black neighborhoods), a mosque, many synagogues (including two yeshivas), and other places of worship; the level of religious diversity in the city is high.^{[citation needed]}

A study of the demographics of the New Haven metro area, based on age, educational attainment, and race and ethnicity, found that they were the closest of any American city to the national average.