In 1792, the year after Saratoga County was founded, the New York State Legislature divided “Balls Town” into four parts forming three new towns: Galway, Milton and, in the southwest corner of the county, Charlton. Previously Charlton had been called "New Freehold" by its settlers who were mostly immigrants from Freehold, New Jersey.  Why the name Charlton was chosen, or where it came from, is not known. It may have been for John Charlton, a squatter already living in the area when early settlers arrived.  The Town had close to 1,500 residents and held its first Town meeting on April first.

First settlers in the southern part of West Charlton were the Gonzales, a Spanish Huguenot family farming there in 1770.  Starting in 1774, Episcopalian and Presbyterian families from Freehold, NJ and downstate NY settled eastern Charlton. Settlers from Scotland arrived in West Charlton in 1775.  French Huguenots, Dutch, Irish and others followed.  Research on northern West Charlton shows land first deeded from Native Americans in 1708 and a stage route through a busy hamlet during the 1700s, but the date of first settlement there remains to be established.

From the start, agriculture has been Charlton's main industry.  Several hamlets with a variety of mills, shops, taverns, schools, churches and cemeteries formed along the Town’s waterways and stage routes.  These community centers came to be known as New Freehold (Charlton Hamlet), Slab Troy (Little Troy), Liberty Three Corners (West Charlton), Scotch Street (Scotch Church), Blue Corners, Holbrook Corners and Harmony Corners. In 1865, Charlton's population had changed little: 1,589 people living in 333 dwellings.

Charlton may be considered small in size but is vast in agricultural resources and has been fortunate to retain its rural beauty.  Agriculture continues as the town’s main industry.

According to the 2010 Census, Charlton’s population has increased 4.5% since the 2000 census; the Town now has 4,133 residents.  Families represent 84.3% of the population giving Charlton a higher than average concentration of families.  Median age for residents is 42.2 which is older than the average age in the U.S.  Five public school districts serve the Town.  Charlton has six postal ZIP codes spread across three counties.  Three of seven churches remain, and there is a chapel at the Charlton School (a residential school for young women with special needs).  There are three fire districts in Charlton as well as five parks, and eleven cemeteries.  A Town Board consisting of a supervisor and four councilmen meet twice monthly.  Charlton does not have a Town tax.

Much of Charlton’s population increase came with residential areas built in the mid-twentieth century in the southeastern part of town.  The stagecoach routes that connected the hamlets were straightened and paved; and now all of the mills are gone.  Few shops and one tavern remain.  Land sub-divisions and property sales throughout the Town have brought many more new homes and residents.

Education has always been important to the people of Charlton.  In the late 1700s citizens helped to found Union College to educate leaders of the new United States.  Three well-known first graduates of the College were from Charlton. Gideon Hawley, successful lawyer and businessman, founded New York State’s public education system. In response to his 1812 New York State Law for the establishment of common schools, Charlton setup ten one-room school districts so that no child had to walk more than a mile to school.  Joseph Sweetman, a Charlton minister for seventy-one years, spread the Presbyterian Church throughout the Northeast and into Canada.  John W. Taylor, Attorney-at-Law, served as both New York Senator and Assemblyman, and was twice Speaker of the United States House of Representatives in its formative years.

There is Town-wide interest in preserving Charlton’s heritage.  Presently eighteen historic markers and other signage mark places of importance.  The Charlton Historic District, New York State’s first rural hamlet historic district, and Scotch Church Historic Site are listed on the New York State and National Registers of Historic Places. They may also be found on related websites. The Historic District has a Historic Main Street Improvement Plan, and the Town acknowledges significance of its history in the Comprehensive Plan.

For fifteen years students and faculty advisors of the Burnt Hills-Ballston Lake Richard O’Rourke Middle School have helped to place flags at veterans’ graves in Charlton cemeteries for Memorial Day.  More than 240 graves receive flags. The Charlton Historical Society sponsors an annual Memorial Day ceremony in Gideon Hawley Park, which is followed by an annual Founder’s Day celebration, during the first weekend of June.  There are special community activities, fireworks, and a Sunday afternoon parade. The Sons and Daughters of Liberty Ancient Fifes and Drums were founded in Charlton in 1975 and continues its unending commitment to portraying the early history of our nation through music and historical re-enactment.

2004 saw a significant step to permanently preserve and protect farmland, forests, and riverbanks in Charlton.  Acreage was donated as a conservation easement to Saratoga P.L.A.N. to protect Charlton's landscape heritage to help retain its rural character.

In 2006, the Town broke ground and built a new Town Hall in the Historic District. The new Town Hall was built with funds that previous Town Boards and the current Board had put aside over the years specifically for this purpose. Care was taken to safeguard historic and archaeological resources, and to preserve community character. The interior of the old Town Hall has been somewhat updated and is now used as a Community Center...the outside of the building remains the same.