Benthorn used to be a heerlijkheid (manor), owned by the States of Holland and West Friesland. It was sold to Adam Adriaan van der Duyn, lord of 's Gravemoer, in 1724.[1] In 1812, Benthorn became a part of the municipality of Hazerswoude, but on 1 April 1817 it became a separate municipality again.[2]
According to the 19th-century historian A.J. van der Aa, in 1840 Benthorn consisted of 0.85 square km and had 10 inhabitants in 2 houses.[1] Because of the small size of the municipality, it was merged into Benthuizen in 1847.[2]
Part of the hamlet had to be demolished for the construction of the high speed railway HSL-Zuid, and only three farms remain. The name of the hamlet no longer appears on recent topographical maps of the area.[3]