The history of the church probably starts at the end of the 12th century, with a three-aisled vaulted cruciform basilica which at that time has the title of chapel only and is mainly used by the fishermen and tradesmen who have settled at the banks of the river Aa. In the 13th century permission is granted to use the building as a parish church, named Onze Lieve Vrouwe ter Aa (Church of Our Lady ter Aa), although the church is also dedicated to St. Nicolaas, protector of sailors.
The current church is largely the result of a major transformation of this Romanogothic church into a Gothic one. It started with a new choir in 1452, which is very similar to that of the Martinikerk, and after heightening of the transept and the addition of side-aisles little was left of the old church. After the Reformation in 1594 catholicism was banned, and the name of the church was shortened to Der Aa-kerk or even A-kerk. In 1671 lightning struck the tower, destroying its upper part and the western vaults of the nave. The tower was rebuild in such an amateuristic fashion that in 1710 it collapsed, destroying part of the nave. A new tower in Classical style was built where the destroyed part of the nave used to stand. The colourful upper part was designed by town architect Allert Meijer and was completed in 1718.
A big restoration was started in 1975 and was completed in 1987. In that year the church-counsil handed the building to a seperate foundation that now maintains it and rents it for all sorts of events.