The school was founded in 1558 and named after Thomas Alleyne, who was rector of Stevenage. In his will, Thomas Alleyne left money that was used to found Master Allen's school. The name was changed to Alleyne's Grammar School in 1869.
20th Century Francis Cammaerts (1916–2006), French Resistance leader and witness in the ''Lady Chatterley's Lover'' Trial, was headmaster from 1952 to 1961.
Francis Cammaerts was the author
Michael Morpurgo's uncle. Morpurgo wrote a fictional story based on his uncle's experiences in WWII 'In the Mouth of the Wolf'. The
Vincent motorcycle factory was based in the current Thomas Alleyne Academy reception between 1928 and 1955. There is a plaque on the reception building commemorating the Vincent motorcycle champion
George Brown In 1969 the school became a comprehensive, '''Alleyne's School'''. In 1989 it merged with Stevenage Girls' School and changed to its name to Thomas Alleynes School.
21st Century In 2008, the school became a Specialist Science College and received funding from the Department for Children, Schools and Familie to upgrade Science and ICT facilities. During the summer of 2012, Thomas Alleyne's was chosen to choose a torchbearer to run with the torch for the
2012 Summer Olympics. The school became an
Academy in 2013, in partnership with the Hart School Trust The school is still on the site it has occupied for four and a half centuries, a short walk both from Thomas Alleyne's Church and from his home. ==Academy Status==