The parish was historically part of the manor of Carlton in the large parish of Coverham. At some time the manor was divided into two manors (and townships), Carlton Town (the village of Carlton) and Carlton Highdale (the remaining part). In 1866 the township became a separate civil parish.
Prior to the nationwide municipal reorganization of 1974, Carlton Highgate was located in Leyburn Rural District. Historically, it was located in the ecclesiastical parish of Coverham in the Hang West Wapentake.