Prior to European colonization, the area today known as Lynn was inhabited by the Naumkeag people. The English settled Lynn not long after the 1607 establishment of Jamestown, Virginia—the first successful English colony in North America—and the 1620 arrival of the Mayflower at Plymouth. European settlement of the area was begun in 1629 by Edmund Ingalls, followed by John Tarbox of Lancashire in 1631. The area today encompassing Lynn was originally incorporated in 1629 as Saugus, the Nipmuck name for the area. Three years after the settlement in Salem, five families pushed into the wilderness of Lynn, then Saugust, and the Tomlin family constructed a large mill between today's Sluice and Flax Ponds. The mill not only supplied grains and sustenance for the settlers and trade with the Naumkeag people, but was used to create brews and many fermented casks of hops and wines to send back to King George in England.

A noteworthy early Lynn colonist, Thomas Halsey, left Lynn to settle the East End of Long Island, where he and several others founded the Town of Southampton, New York. The resulting Halsey House—the oldest extant frame house in New York State (1648)—is now open to the public, under the aegis of the Southampton Colonial Society.

Further European settlement of Lynn led to several independent towns being formed, with Reading created in 1644; Lynnfield in 1782; Saugus in 1815; Swampscott in 1852; and Nahant in 1853. The City of Lynn was incorporated in 1850, taking its name from King's Lynn, Norfolk, England, in honor of Samuel Whiting.

Colonial Lynn was an early center of tannery and shoe-making, which began in 1635. The boots worn by Continental Army soldiers during the Revolutionary War were made in Lynn, and the shoe-making industry drove the city's growth into the early nineteenth century. This legacy is reflected in the city's seal, which features a colonial boot.

In 1816, a mail stage coach was operating through Lynn. By 1836, 23 stage coaches left the Lynn Hotel for Boston each day. The Eastern Railroad Line between Salem and East Boston opened on August 28, 1838. This was later merged with the Boston and Maine Railroad and called the Eastern Division. In 1847 telegraph wires passed through Lynn, but no telegraph service station was built until 1858.

During the middle of the nineteenth century, estates and beach cottages were constructed along Lynn's shoreline, and the city's Atlantic coastline became a fashionable summer resort. Many of the structures built during this period are today situated within the National Register-listed Diamond Historic District.

Further inland, industrial activity contemporaneously expanded in Lynn. Shoe manufacturers, led by Charles A. Coffin and Silas Abbott Barton, invested in the early electric industry, specifically in 1883 with Elihu Thomson, Edwin J. Houston, and their Thomson-Houston Electric Company. That company merged with Edison Electric Company of Schenectady, New York, forming General Electric in 1892, with the two original GE plants being in Lynn and Schenectady. Coffin served as the first president of General Electric.

Initially the General Electric plant specialized in arc lights, electric motors, and meters. Later it specialized in aircraft electrical systems and components, and aircraft engines were built in Lynn during WWII. That engine plant evolved into the current jet engine plant during WWII because of research contacts at MIT in Cambridge.Gerhard Neumann was a key player in jet engine group at GE in Lynn. The continuous interaction of material science research at MIT and the resulting improvements in jet engine efficiency and power have kept the jet engine plant in Lynn ever since.

One of the largest strikes of the early labor movement began in the shoe factories of Lynn on February 22, 1860, when Lynn shoemakers marched through the streets to their workplaces and handed in their tools, protesting reduced wages. Known as the New England Shoemakers Strike of 1860, it was one of the earliest strikes of its kind in the United States.

In 1841, abolitionist Frederick Douglass, moved to Lynn as a fugitive slave. Douglass wrote his first autobiography, Narrative of the Life of Frederick Douglass, an American Slave, while living in Lynn. The publication would become Douglass' best-known work. Douglass, his wife, and their five children lived in Lynn until 1848.

On February 1, 1866, Mary Baker Eddy experienced the "fall in Lynn", often referred to by Christian Scientists as significant to the birth of their religion.

Lynn experienced a wave of immigration during the late 1800s and early 1900s. During the 30 years between 1885 and 1915, Lynn's immigrant population increased from 9,800 to 29,500, representing nearly one-third of the city's total population. Polish and Russian Jews were the largest single group, numbering more than 6,000. The first Jewish settlers in Lynn, a group of twenty Hasidic European families, mostly from Russia, formed the Congregation Anshai Sfard, a Hasidic, conservative Jewish synagogue in 1888. Catholic churches catering to the needs of specific language and ethnic groups also testify to the waves of immigrants. St. Jean Baptiste parish, eventually including a grammar school and high school, was founded in 1886, primarily for French-Canadians. Holy Family Church conducted services in Italian beginning in 1922, and St. Michael's church also provided church services and a grammar school for the Polish-speaking community, beginning in 1906. St. Patrick's church and school was a focus of the Irish-American community in Lynn. St. George's Greek Orthodox Church was founded in Lynn in 1905. Later in the 20th century, the city became an important center of greater Boston's Latino community. Additionally, several thousand Cambodians settled in Lynn between 1975 and 1979 and in the early 1980s.

At the beginning of the 20th century, Lynn was the world-leader in the production of shoes. 234 factories produced more than a million pairs of shoes each day, thanks in part to mechanization of the process by an African-American immigrant named Jan Ernst Matzeliger. From 1924 until 1974, the Lynn Independent Industrial Shoemaking School operated in the city. However, production declined throughout the 20th century, and the last shoe factory closed in 1981.

In the early 1900s, the Metropolitan District Commission acquired several coastal properties in Lynn and Nahant, in order to create Lynn Shore and Nahant Beach Reservations, and to construct adjoining Lynn Shore Drive. When it opened to the public in 1910, Lynn Shore Drive catalyzed new development along Lynn's coastline, yielding many of the early 20th century structures that constitute a majority of the contributing resources found in the National Register-listed Diamond Historic District.

During the late 1970s and early 1980s, Lynn suffered several large fires. On November 28, 1981, a devastating inferno engulfed several former shoe factories, located at Broad and Washington Streets. Seventeen downtown buildings were destroyed, with property losses totaling in the tens of millions of dollars. (The affected area has since been largely redeveloped into a satellite campus of North Shore Community College, with many adjacent warehouses converted to loft apartments.)

A reputation for crime and vice gave rise to a taunting rhyme about Lynn which became popular throughout Eastern Massachusetts: "Lynn, Lynn, the city of sin, you'll never come out the way you went in, what looks like gold is really tin, the girls say 'no' but they'll give in, Lynn, Lynn, the city of sin." Another variation was "Lynn, Lynn the city of sin: if you ain't bad, you can't get in!"

In order to counter its reputation as "the city of sin", Lynn launched a "City Of Firsts" advertising campaign in the early 1990s, which promoted Lynn as having:

Some of these claims were subsequently found to be inaccurate or unprovable.^{[citation needed]}

In a further effort to rebrand the municipality, city solicitor Michael Barry proposed renaming the city Ocean Park in 1997, but the initiative was unsuccessful.

Despite losing much of its industrial base during the 20th century, Lynn remained home to a division of General Electric Aviation; the West Lynn Creamery (now part of Dean Foods's Garelick Farms unit); C. L. Hauthaway & Sons, a polymer producer; Old Neighborhood Foods, a meat packer; Lynn Manufacturing, a maker of combustion chambers for the oil and gas heating industry; Sterling Machine Co.; and Durkee-Mower, makers of "Marshmallow Fluff".

In the early 2000s, the renovation and adaptive re-use of downtown historic structures, together with new construction, launched a revitalization of Lynn, which remains ongoing. Arts, culture, and entertainment have been at the forefront of this revitalization, with new arts organizations, cultural venues, public art projects, and restaurants emerging in the downtown area. In 2012, the Massachusetts Cultural Council named downtown Lynn one of the first state-recognized arts and culture districts in Massachusetts.

In 2015, Massachusetts Governor Charlie Baker established a task force, composed of representatives of multiple state and municipal public agencies, to further Lynn's revitalization.

Formerly vacant industrial buildings continue to be converted into loft spaces, and historic homes, particularly Lynn's Diamond Historic District, are being restored. In 2016, several large land parcels in Lynn were acquired by major developers. In November 2018, construction began on downtown Lynn's first luxury midrise—a 259-unit, 10-story building on Monroe Street. in December 2019, ground was broken on a 331-unit waterfront development on Carroll Parkway. Many of the recent and pending large real estate projects in Lynn are Transit-oriented developments, sited within a half-mile of Lynn station, which provides 20-minute train service to North Station.

Lynn's revitalization has been bolstered by the city's emergence as a center of creative placemaking. In 2017, swaths of the city's downtown were transformed by a series of large-scale murals, painted on buildings by local, national, and international artists, as part of the city's inaugural Beyond Walls festival. Light-based interventions, including projections onto High Rock Tower, the installation of vintage neon signs on downtown buildings, and large-scale LED-illuminations of the Massachusetts Bay Transportation Authority rail underpasses bisecting Lynn's Downtown, also have been deployed. In 2017, Mount Vernon Street, in the core of the downtown Central Square area, began to host block parties, food trucks, and other special events.

In recent years, Lynn has attracted a substantial and growing LGBT population.

In April 2018, The Boston Globe named Lynn one of the "Top spots to live in Greater Boston in 2018."

As of the census of 2010, there were 90,329 people, 33,310 households, and 20,988 families residing in the city.

The racial makeup of the city was:

Hispanic or Latino of any race were 32.1% of the population (10.5% Dominican, 6.3% Guatemalan, 5.4% Puerto Rican, 2.8% Salvadoran, 1.7% Mexican, 0.6% Honduran, 0.4% Colombian, 0.4% Spanish, 0.2% Peruvian, 0.2% Cuban).

Cambodians form the largest Asian origin group in Lynn, with 3.9% of Lynn's total population of Cambodian ancestry. Other large Asian groups are those of Vietnamese (1.0%), Indian (0.4%), Chinese (0.3%), and Laotian (0.2%) ancestry.

In the city, the population was spread out, with 24.9% under the age of 18 and 75.1% over 18. Males accounted for 49% and females 51%.

Between 2009 and 2013, the median household income in Lynn was $44,849. The per capita income was $22,982. About 21.0% of the population was considered below the poverty line.

In 1990 Lynn had 2,993 persons of Asian origin. In 2000 Lynn had 5,730 Asians, an increase of over 91%, making it one of ten Massachusetts cities with the largest Asian populations. In 2000 the city had 3,050 persons of Cambodian origin, making them the largest Asian subgroup in Lynn. That year the city had 1,112 persons of Vietnamese origin and 353 persons of Indian origin. From 1990 to 2000 the Vietnamese and Indian populations increased by 192% and 264%, respectively.

By 2004 the Cambodian community in Lynn was establishing the Khmer Association of the North Shore.

Data is from the 2009–2013 American Community Survey 5-Year Estimates.