Stephen Hawking School opened following a review of provision for children with severe learning difficulties in Tower Hamlets in the 1990s. This review recommended that the all-ages school should close and two new schools, one primary and one secondary, should open in its place. As a result, Stephen Hawking School opened as a 75 place school for children with severe and profound and multiple learning difficulties in September 1996 with just 24 pupils on roll.

In 1996, prior to the school opening, the governors contacted Professor Stephen Hawking to ask him for permission to name the school after him. They expressed a desire to name the school after someone who had shown amazing achievement in the face of significant adversity. Professor Hawking responded saying that he would be delighted if the school was named after him. Unfortunately, he was never able to visit.

In 2001 the designation of Stephen Hawking School changed to a school for children with profound and multiple learning difficulties.

Following a successful bid in 1999 the school governors set up the Stephen Hawking School Trust, now also known as ‘Whoosh!’. The purpose of this charity is to provide support and training for children and their families. Currently, this is mainly done via clubs after school.

In 2009 Stephen Hawking School started an Outreach Service to support children with severe learning difficulties in mainstream schools. This service is extremely successful and currently has a waiting list.

In 2015-2016, the school had grown and needed to accommodate between 95-100 pupils. Following discussions with the Local Authority, it was agreed for Stephen Hawking School to move to two sites to provide a more appropriate environment for all children. As a result, Stephen Hawking School opened its site at St Jude’s Road in 2018.