The school was named after William Barcroft, the son of a clergyman who was a student at Sydney Sussex College Cambridge from 1708-1715. William Barcroft set up a bursary for students from poorer families to assist their sons through university. The college owned land in Cleethorpes and many of the local streets are named after prominent former students at the College.

The original Barcroft Street School was built between January and late August 1896. The school opened in September 1896 and very soon had 1200 pupils on role. The original school cost £12000 to build. In 1989 the school became a Grade II listed building.

In 1908 the opening of Elliston School reduced the number on role. In 1952 Queen Mary Infants School opened and the school served children aged 7-11.

William Barcroft Junior School was built on the site of the old school playing fields off Barnett Place in 1993. The school cost £1.4 million to build and was the last school built by Humberside County Council. The school opened to pupils on July 5th 1993, with 310 pupils on role. The school was officially opened by County Councillor Don Rose in October 1993.

The school was originally built in a figure of eight design with ten classes. There have since been a number of extensions and the school now has eleven classrooms, ICT Suite, Music Room and Video Conferencing facilities.