Historically, Waplington was in the ecclesiastical parish of Allerthorpe in the wapentake of Harthill. From 1894 until 1935, Waplington was a civil parish in the Pocklington Rural District. In 1935 the civil parish was abolished and the area was merged with the civil parish of Allerthorpe.
In 1974 most of what had been the East Riding of Yorkshire was joined with the northern part of Lincolnshire to became a new English county named Humberside. The urban and rural districts of the former counties were abolished and Humberside was divided into non-metropolitan districts. The new organization did not meet with the pleasure of the local citizenry and Humberside was wound up in 1996. The area north of the River Humber was separated into two "unitary authorities"—Kingston-upon-Hull covering the former City of Hull and its closest environs, and the less urban section which, once again, named itself the East Riding of Yorkshire.