Little Staughton, known at the beginning of the 11th century as Stoctun from the old english meaning "farmstead at an outlying hamlet". It was referred to in the Doomsday book simply as Staughton, although it does not refer to any taxes being collected in the area. However, by the time of the Heath tax return in 1671, there were approximately 250 individuals living there. The population rose to a peak of 572 in 1861, then fell due to 218 by 1951, due to the industrial revolution and two World Wars.

The Church of All Saints, previously dedicated to St Margaret's, originally had a spire that was destroyed by lightning. The building has been Grade I listed since 1964.

During World War II it was the home of 109 Squadron (Mosquito bombers) and 582 Squadron (Lancaster bombers) at RAF Little Staughton. The airfield is now largely used for other purposes but retains a recently listed Control tower. In January 2020, Little Staughton Airfield and Industrial Park applied for planning permission to develop the site to re-open the airfield.