Originally granted by the Massachusetts General Court to veterans of New England's first war with Canada from Salem, Massachusetts, the area was known as Salem-Canada. John Cram and his family were the first settlers, and established a sawmill in the community in 1736. The name Lyndeborough resulted from a re-grant to a group of people that included Benjamin Lynde, who later became Chief Justice of Massachusetts. This group of proprietors never lived in Lyndeborough and may never have visited the community. For instance, while serving as a proprietor of Lyndeborough, Judge Lynde lived in Massachusetts, where he presided in Suffolk County over the trial stemming from the Boston Massacre.

The town has been home to the Lafayette Artillery Company (founded 1804) since 1833. The town office building, Citizens' Hall (opened 1889), is listed on the National Register of Historic Places, as is the Lyndeborough Center Historic District, which consists of the Congregational Church (circa 1836), Town Hall (1846), and remnants of the Town Pound (1774).

According to the United States Census Bureau, the town has a total area of 30.5 square miles (79 km²), of which 30.4 square miles (79 km²) is land and 0.1 square miles (0.26 km²) is water, comprising 0.38% of the town. The highest point in Lyndeborough is just shy of 1,800 feet (550 m) above sea level, where the east ridge of North Pack Monadnock Mountain crosses the town's western border. Notable summits in town include Winn Mountain (1,686 ft or 514 m), Rose Mountain (1,730 ft or 530 m), and The Pinnacle (1,703 ft or 519 m).

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