Nathaniel Allen (1780 – December 22, 1832) was an American politician, and a United States representative from New York.

He married Hilzibeth Akin and they had four children, Nathaniel, John, Hilzebeth, and Almira.

He was commissioner and paymaster on the Niagara frontier in 1812, and was a militia officer during the War of 1812 as was his brother, Peter Buell Allen.

He engaged in the prosecution of claims for money due in connection with the construction of the Louisville & Portland Canal.

Allen died in the Galt House hotel, while conducting business in Louisville, Kentucky, on December 22, 1832 (age about 52 years).