The school opened on its current site with a brand new building and two mobile classrooms in September 1982. Since then, there has been extensive building work, resulting in all classes now being housed in the main building. There have been internal modifications, with the building of partitioning walls between classes, and a purpose-built music and drama room has been added in recent years. The grounds have been extensively developed to provide a range of outdoor play equipment and garden areas.
The Junior School can trace its origins back to the Junior Department of Sawtry United District Board School, which was opened on Monday, 1st. May, 1876 by J.M. Heathcote of Conington Castle. The original school building is now the Old School Hall owned by the Parish Council.
The first school educated children from the age of 5 to 12 years. The Bye-Laws stated that the ordinary payment from each scholar should not exceed 9d. (31/2 pence) per week. The curriculum consisted of the 3-R's, reading, writing and arithmetic alongside vocational and traditional skills. The girls were expected to become competent at needlework and were taught to make shirts from calico. Boys were taught basic horticultural skills to prepare them for their working lives.
Although its visitors reported the school as being a happy and industrious place there were obvious difficulties for the two teachers, two pupil teachers and one monitress in teaching over 200 pupils. Not surprising then, when the Inspectors visited in 1884 they reported that "the school shows fair order and fair results in the elementary subjects. Grammar is a failure". Discipline was necessarily strict with classes of up to 65 children. Corporal punishment probably deterred most errant behaviour although in 1890 after a boy assaulted a master he was not only expelled but prosecuted and fined 10 shillings with £1 costs.
The grants the school received were based upon attendance. Ensuring that children attended school was always a problem, particularly at harvest time when there was work to be done in the fields. Low attendance in November 1914 was accounted for by the "fact that scholars over twelve years of age are now permitted to go to agricultural work because of the shortage of normal labour due to the war". Health problems also affected the number attending school. The Medical Officer frequently closed the school because of epidemics of whooping cough and influenza. In 1880 only 36 pupils out of 210 were in school because of an outbreak of measles.
Changes in education policy and the need for more space led to the Village College being opened in 1963 and the Infant School in 1972. The old school was eventually closed upon completion of the new open plan Junior School that opened in September.
The school joinined Cambridge Meridian Academies Trust (CMAT) and became an Academy on Tuesday 1st November 2016. The new Academy has been named Sawtry Junior Academy.