The Suffolk County Historical Society was founded in 1886 by a group of forward-looking county residents.

The Civil War had recently ended; the country had just celebrated its Centennial; and Americans were thinking about their heritage and how to preserve it. The founders of the society realized that in a rapidly changing world, if something were not done to record the county’s history it would soon be lost. The County Seat of Riverhead was chosen as the logical place to found the new society, and County Surrogate Judge James H. Tuthill became the first President. The society began collecting items almost immediately, and the first displays were placed in a small glass case in Tuthill’s Riverhead office.

The society's collection soon outgrew the Judge's office, and in 1893 a small building at the corner of Griffing Avenue and Main Street in Riverhead, which formerly housed the County Clerk's Office, was purchased. The growing collection of documents and artifacts soon outgrew that space too. In the 1920’s Mrs. Alice O. Perkins, widow of John Perkins, and a member of one of Riverhead’s prominent families, gave a parcel of land facing the Peconic River at the western portal of the village of Riverhead to the society for the erection of a building within five years time, which compelled the construction of the central section of the present museum building in 1930. The East and West wings were added in 1951, through a gift made by Cora Reeves Barnes, and in 1964 the North wing was built, made possible by a gift from Sylvia Staas, in memory of her mother Elizabeth Downs Staas.