The site on which St Helen's now stands was probably important from the time that the Roman army first established a legionary headquarters in the city in 71 AD. The main gateway into the city was at the far corner of what is now St Helen's Square (the former churchyard). From there the main street (Via Praetoria) to the military and administrative headquarters of the Roman province, on the site of what is now The Minster, ran approximately along the line of Stonegate. You can just see Stonegate on the left of the picture above. A site like this would often be occupied by an important building such as a temple and we can only speculate what remains might lie beneath the present church.
Although the first evidence we have of St Helen's dates only from the twelfth century, it is probably of pre-Conquest origin, ie from the first half of the eleventh century or significantly earlier. The alignment of the church (at an angle to the adjacent streets) corresponds to the presumed alignment of the Anglo-Saxon Minster. St Helen was revered within the Anglo-Saxon church from at least the eighth century, and the destroyed church of St Helen Aldwark was certainly a pre-Conquest foundation.
Churches in pre-Conquest York seem to have been numerous. Even in the later middle ages there were still over forty in the city. These churches were generally small and apparently often founded not to serve the local population, or parish, but funded by a patron as an act of religious devotion. The first St Helen's may have been built of wood, and it stood in a churchyard extending over much of what is now St Helen's Square and probably fronting Stonegate.
The twelfth to sixteenth century
The oldest datable feature in the church is the mid twelfth century font, and it is likely that the church was rebuilt in stone at that time or earlier. A few fragments of reused twelfth and more certainly thirteenth century masonry provide evidence of successive building phases, growing the church from what in the Saxon period will have been a small rectangular building within the present nave. There was major work in the fourteenth century and again in the fifteenth; probably adding and then altering the aisles and giving the floor plan we have today, with aisles north and south of the nave, though the chancel was only added in 1857. The glass now in the west window seems to be but a vestige of what was in the church and the interior will have been painted and decorated.
Despite the care and money clearly expended on the church, it had a very small parish of only a couple of hundred houses, and little income to support the priest. Other city churches closed, including at least two others dedicated to St Helen. With the Reformation, the closing of the monasteries, and changes to the way religion was taught and observed, came further rationalisation. With so many other churches close by, including St Martin in Coney Street and St Michael le Belfry at the other end of Stonegate, the case for closure of St Helen's must have seemed a strong one and in 1552 the church was sold and partly demolished. A public outcry ensured that was not the end of the story.