The area around the meeting house and along the Stony Brook river was originally the "Stony Brook Village," officially part of the town of West Windsor in Middlesex County. A majority of the original colonists that came to settle in Stony Brook were Quaker farmers who purchased much of the land along the Stony Brook river from proprietors Thomas Warne and William Penn. Initially, the Quakers met for worship in private homes, but in 1709, Benjamin Clarke gave nine acres of land to Richard Stockton and his fellow trustees of the Chesterfield Monthly Meeting of Friends.
On this spot, the trustees laid out a gravesite and in 1724 - the same year Princeton was given its name - Quaker stonemasons set to work on the Stony Brook Meeting House, which stands today. It was gutted by fire in 1758, but was quickly repaired. In 1838, Stony Brook became a part of the new Princeton Township.
During the Battle of Princeton, the meeting house was used as an infirmary for both British and American soldiers. In 1781, a school was established by the Quaker Friends society, which met in the schoolmaster's house on Quaker Road. In 1800, a schoolhouse was built next to the meeting house; the structure was torn down a century later.