Once part of Algonquian territory, Brookline was first settled by European colonists in the early 17th century. The area was an outlying part of the colonial settlement of Boston and known as the hamlet of Muddy River. In 1705, it was incorporated as the independent town of Brookline. The northern and southern borders of the town were marked by two small rivers or brooks, which is the town’s namesake. The northern border with Brighton (which was itself part of Cambridge until 1807) was Smelt Brook. (That name appears on maps starting at least as early as 1852, but sometime between 1888 and 1925 the brook was covered over.) The southern boundary, abutting Boston, was the Muddy River.

The Town of Brighton was merged with Boston in 1874, and the Boston-Brookline border was redrawn to connect the new Back Bay neighborhood with Allston-Brighton. This merger created a narrow strip of land along the Charles River belonging to Boston, cutting Brookline off from the shoreline. It also put certain lands north of the Muddy River on the Boston side, including what are now Kenmore Square and Packard's Corner. The current northern border follows Commonwealth Avenue, and on the northeast, St. Mary's Street. When Frederick Law Olmsted designed the Emerald Necklace of parks and parkways for Boston in the 1890s, the Muddy River was integrated into the Riverway and Olmsted Park, creating parkland accessible by both Boston and Brookline residents.

Throughout its history, Brookline has resisted being annexed by Boston, in particular during the Boston–Brookline annexation debate of 1873. The neighboring towns of West Roxbury and Hyde Park connected Brookline to the rest of Norfolk County until they were annexed by Boston in 1874 and 1912, respectively, putting them in Suffolk County. Brookline is now separated from the remainder of Norfolk County.

Brookline has long been regarded as a pleasant and verdant environment. In the 1841 edition of the Theory and Practice of Landscape Gardening, Andrew Jackson Downing described the area this way:

Brookline residents were among the first in the country to propose extending the vote to women. Benjamin F. Butler, in his 1882 campaign for Governor, advocated the idea.

In 1843, the town legally banned resales of deeds to "any negro or native of Ireland."

Two branches of upper Boston Post Road, established in the 1670s, passed through Brookline. Brookline Village was the original center of retail activity. In 1810, the Boston and Worcester Turnpike, now Massachusetts Route 9, was laid out, starting on Huntington Avenue in Boston and passing through the village center on its way west.

Steam railroads came to Brookline in the middle of the 19th century. The Boston and Worcester Railroad was constructed in the early 1830s, and passed through Brookline near the Charles River. The rail line is still in active use, now paralleled by the Massachusetts Turnpike. The Highland Branch of the Boston and Albany Railroad was built from Kenmore Square to Brookline Village in 1847, and was extended into Newton in 1852. In the late 1950s, this would become the Green Line D branch.

The portion of Beacon Street west of Kenmore Square was laid out in 1850. Streetcar tracks were laid above ground on Beacon Street in 1888, from Coolidge Corner to Massachusetts Avenue in Boston, via Kenmore Square.^{[citation needed]} In 1889, they were electrified and extended over the Brighton border at Cleveland Circle. They would eventually become the Green Line C branch.

Thanks to the Boston Elevated Railway system, this upgrade from horse-drawn carriage to electric trolleys occurred on many major streets all over the region, and made transportation into downtown Boston faster and cheaper. Much of Brookline was developed into a streetcar suburb, with large brick apartment buildings sprouting up along the new streetcar lines.

Brookline was known as the hamlet of Muddy River and was considered part of Boston until the Town of Brookline was independently incorporated in 1705. (The Muddy River was used as the Brookline–Boston border at incorporation.) It is said that the name derives from a farm therein once owned by Judge Samuel Sewall. Originally the property of CPT John Hull and Judith Quincy Hull. Judge Sewall came into possession of this tract, which embraced more than 350 acres, through Hannah Quincy Hull (Sewall) who was the Hull's only daughter. John Hull in his youth lived in Muddy River Hamlet, in a little house which stood near the Sears Memorial Church. Hull removed to Boston, where he amassed a large fortune for those days. Judge Sewall probably never lived on his Brookline estate.

As of the census of 2010, there were 58,732 people, 24,891 households, and 12,233 families residing in the town. The population density was 8,701.0 people per square mile (3,247.3/km²). There were 26,448 housing units at an average density of 3,889.6 per square mile (1,501.9/km²). The racial makeup of the town was 73.3% White, 3.4% Black or African American, 0.12% Native American, 15.6% Asian (6.7% Chinese, 2.6% Indian, 2.3% Korean, 1.8% Japanese), 0.03% Pacific Islander, 1.01% from other races, and 3.0% from two or more races. Hispanic or Latino of any race were 5.0% of the population (0.9% Mexican, 0.8% Puerto Rican). (Source: 2010 Census Quickfacts)

There were 25,594 households, out of which 21.9% had children under the age of 18, living with them, 38.4% were married couples living together, 7.1% had a female householder with no husband present, and 52.2% were non-families. 36.7% of all households were made up of individuals, and 10.1% had someone living alone who was 65 years of age or older. The average household size was 2.18 and the average family size was 2.86.

In the town, the population distribution was wide, with 16.6% under the age of 18, 11.7%, from 18 to 24, 37.3% from 25 to 44, 21.9% from 45 to 64, and 12.4% who were 65 years of age or older. The median age was 34 years. For every 100 females, there were 82.6 males. For every 100 females age 18 and over, there were 79.1 males.

The median income for a household in the town was $66,711, and the median income for a family was $92,993. Males had a median income of $56,861 versus $43,436 for females. The per capita income for the town was $44,327. About 4.5% of families and 9.3% of the population were below the poverty line, including 5.3% of those under the age of 18 and 7.5% of those ages 65 and older.

Serving as a residential zone for nearby academic and medical institutes such as Harvard Medical School and Boston University, Brookline was reported as the town with the most doctoral degree holders (14.0% of the total population in 2012) in the United States.