The school was originally sited in Ipswich town centre, next to St Pancras Church on Cox Lane. It was founded in 1871 and provided for some of the poorest people in Ipswich, many of Irish immigrant origins. The stone on display at the front entrance of the school today has an inscription Enlarged 1886.

In the late 1950s it was decided to re-locate the school on Stratford Road, in the expanding north-west suburbs of Ipswich. The school was re-opened on September 16th 1957. On the 21st March 1958 the school was formally opened and blessed by His Lordship, the Bishop of Northampton. At this point it only had three classrooms, the three off the main corridor.

On the 24th April 1961 work began on a large extension to the school, comprising a large assembly hall and two additional classrooms. On the 12th October 1961, with the extension then complete and in use, the school was blessed by His Lordship the Bishop of Alinda, Monsignor Charles Grant, Auxiliary of the Diocese of Northampton. During the ‘baby boom’ years of the 1960s the school had 209 children on roll – an average of over 40 per class! However, during the 1970s and 1980s there was a gradual roll decline.

In the mid-1990s the number of pupils began to increase rapidly again and the Diocese of East Anglia brought in a temporary classroom to enable the school to run six classes. In 1999 a sixth permanent classroom was built off the hall and the school was able to operate as a conventional one-form entry primary with one class per year group.

In 2006-7 a major building and improvement project, supported by the Rope Trust and the Diocese of East Anglia, saw the construction of a new Reception Class, a multi-purpose ‘Mission Room’ and an all-weather sports surface. The following year, in 2008, the school celebrated its Golden Jubilee on Stratford Road. Since then the school has gained from three further significant capital investment projects: a re-modelling of the entrance area, with new offices for the assistant headteacher and headteacher; the re-cladding of the entire south elevation, together with a new classroom, a conference room and two intervention rooms; and a new roof. 

In 2017 the school is one of three Catholic primary schools in Ipswich. The deanery schools are made complete by St. Alban’s Catholic High School, which includes a Sixth Form. Most St. Pancras pupils transfer to St. Alban’s Catholic High School.

In its almost 60 years on Stratford Road, St Pancras has had just eight headteachers: Mr Ted Tynan; Mr Martin Kelly; Mr. Paul Rooney, Mrs Mary Reynolds; Mrs Ann Ball, Mr Stephen Barker, Mr Ian Kearns, and Mrs Lucille Martin who was appointed as Head of School from January 2019.

In April 2019 the school joined the Our Lady of Walsingham Multi Academy Trust.