The church was established by Herbert de Losinga, Bishop of Norwich in 1095 to serve a Benedictine Priory and dedicated to St Margaret of Antioch.

[4] After the English Reformation St Margaret's became the parish church for the town of King's Lynn, and its property was used as an endowment for Norwich Cathedral.

This was reconstructed in a programme of rebuilding between 1745 and 1746 by the architect Matthew Brettingham in an early Gothic revival style.

St Margaret's church was granted the honorary title King's Lynn Minster in 2011 by the Bishop of Norwich.

The main ring of 10 bells is in the key of C with a tenor weighing just over 28 long hundredweight (1,400 kg).