In Roman times, the headquarters of the Roman legionary fort Eboracum was located on the site of today's minister, the remains of which can be seen in the exhibition under the church.
Today's church had at least three previous buildings. No archaeological evidence exists for the first church mentioned by Beda Venerabilis, in which King Edwin was baptized by Paulinus in 627. It was probably made of wood. A stone building, completed about ten years later, was extended by Bishop Wilfrid at the end of the 7th century. It burned down in 741 and was replaced by a stately new building. This church was badly damaged in 1069 when the Anglo-Saxons rebelled against the Norman William the Conqueror and finally destroyed in a Viking invasion in 1075.
In 1080, the first Norman Archbishop, Thomas of Bayeux, began building a Norman church modeled on the Bayeux Cathedral. This survived the city fire damaged in 1137 and was enlarged by additions in the following decades. Walter de Gray, who became Archbishop of York in 1216, began building what is now the Gothic church. The Romanesque church was replaced in sections by the new building. The stumps of the previous building are accessible in the exhibition under the church. There is also the tomb of St. Paulinus.