Brookhaven was originally part of a land grant given to William Penn in 1681 by King Charles II of England. The Proprietor negotiated with the Lenni-Lenape Indians, the original occupants of the land, and then divided the land into municipal districts. The area of Brookhaven was included in the Municipal District of Chester Township. A large land grant of 317 acres was surveyed to Thomas Coebourne who settled there in 1682 along with Richard Few who was granted 227 acres. Thomas Brassey was granted 385 acres in 1684. The original grants were parceled eventually into smaller acreage and sold to subsequent settlers whose names we recognize today, such as Trimble, Edwards, Lister and Shepherd, among others.

For approximately two hundred and fifty years, the region was dependent upon a farming and dairying economy as well as two thriving mill businesses spanning both Chester and Ridley Creeks. Bisected by a major highway, the 1687 Edgmont Great Road, Brookhaven developed as a small crossroads town at Sneath's Corners in the mid-19th century. The road from Hinkson's Corners, now Brookhaven Road, was established sometime before 1816 as a service road to the mills on Ridley and, in 1847, Chester Creeks. At the crossroads of these two highways grew a cluster of services, professional offices and summer homes. The name "Brookhaven" came into common use when it was used in 1872 in the letterhead of the Beatty Brothers General Store at Sneath's (later Beatty's) Corners. The neighborhood attracted numerous doctors and lawyers, and at the turn of the century, was a popular locale for a Sunday outing among residents of the river tier communities.

Brookhaven's mills were perhaps its most notable commercial activity. Thomas Coebourne established the second gristmill in the new colony, successfully challenging William Penn's monopoly vested in the Caleb Pusey mill downstream on Chester Creek. After a 1687 court battle upheld with Coebourne the right for individuals to establish mills, the area's creeks powered a multitude of industries. The original Coebourne log mill was replaced in 1750 by a stone structure which was sold to Jonathan Dutton in 1792. A redrawing of Chester Township's borders in 1829 placed this site in present Middletown Township, with only the mill race and the owner's mansion in Brookhaven. The Johnson Ax Factory, the Lower Bank (Todmorden-Sackville) Hair Cloth Mills, Bickley's Gristmill and the Crozer Cloth Mill all utilized the notable drop for streams from the inland plateau to power their machinery. Both the 1826 and the post-flood 1844 mill surveys show large outputs for these factories.

In the latter part of the 19th century, several large stock farms were thriving; by the 1900s most of these were consolidated under the ownership of John P. Crozer who bred race horses and prize bulls. After Crozer's death and World War II, these farms were sold off to developers. In 1902, the New Chester Water Company built a filtration and storage facility which then serviced the entire city and Township of Chester. This plant, on Harrison's Hill, opposite K-Mart, is still in active use.

The Delaware Valley's rapid industrial expansion and the resulting baby boom of World War II, brought increasing pressure for suburban housing. At the time of Brookhaven Borough's incorporation on April 4, 1945, the Borough had 672 persons and 150 homes. Within fifteen years there was an increase in both of over 400%. New commercial service shops appeared in the 1960s to meet the needs of these new residents. Six shopping centers of various sizes, a medical center and five churches now lie within the Borough's 1.69 square miles. The trolley line which had run from Chester to Media via Edgmont Avenue stopped in 1938; in 1945, its tracks were removed, the road realigned and widened and most of the area's transportation became automotive.

In the last fifty years, Brookhaven has evolved very dramatically from a dairy and stock farm economy to a bustling residential community of over 8,500 people living in over 3,600 homes, apartments and condominiums and supporting approximately 150 businesses.