The earliest reference to St Helen's is in 1235, but the fine mid-twelfth-century font is evidence of greater antiquity. The south arcade may also incorporate some twelfth century masonry. Of the thirteenth century, all that survives is an inverted capital reused as a base in the eastern pier of the north arcade, another inverted capital forming the sub-base of the font, and a quatrefoil base re-used as the base of the font.
The south arcade dates from the fourteenth century - the south aisle being a later rebuild - and there may have been a north aisle of similar date. The east window of c. 1867 is said to have reproduced a previous window design of c. 1300, and the rebuilt square-headed windows of the north aisle could be copied from originals of early fourteenth-century date. The west windows of both north and south aisles (prior to their reconstruction in 1814) also had traceried windows of perhaps comparable date, while the early-mid-fourteenth-century stained glass now in the west window was moved from the original east window in 1857-8. In short, there may have been a major rebuilding of the church in the early fourteenth century, of which only the south arcade now remains more or less intact.
Further substantial work is said to have been carried out in the fifteenth century. Both aisles are said to have been rebuilt then on their present foundations ( though both were entirely rebuilt in the nineteenth century). The west front was also reconstructed, at least in part, in the fifteenth century. The west walls of the aisles may have been retained from the fourteenth century, but the entrance bay closing off the nave was certainly rebuilt with a four-centred arch over the doorway, a four-light Perpendicular window above, and a bell-turret supported on a large over-arch crowning the gable. This survived until 1814.
In the Middle Ages, like most York churches, St Helen's was poorly endowed. At the Reformation, in 1548, it was proposed to unite St Helen's with an adjacent parish, and in 1551-2 the church was sold and partly demolished. However, in 1553-4 an Act was attained to reinstate the church, because it had stood in a `principal place', and its suppression had `defaced and deformed' the city. The present north arcade is thought to belong to the 1550's, and in 1558 money was left towards rebuilding the steeple. St Helen's is thus a very rare example of a parish church whose fabric belongs, in part, to the reign of Queen Mary. The church and parish thus survived, but still on a modest financial basis. In the eighteenth and nineteenth centuries, however, its endowments were supplemented from Queen Anne's Bounty and central funds, and the nineteenth century witnessed three further campaigns on the fabric.
In 1805 and 1814 the west front was restored and rebuilt, following the main lines of the pre-existing structure but on a grander scale, including the pierced and crenellated parapets over the aisle end walls. It was also at this time that the south-west corner of the church was sliced off to form the unusual angled bay which still exists. This campaign gave a far more imposing architectural presence to the church within the urban landscape of St Helen's square.
In 1857-8 extensive work was carried out on the remainder of the fabric under the architect W. H. Dykes. The north aisle was rebuilt, retaining the forms of the previous windows, and the south aisle was rebuilt but introducing tracery patterns based on Decorated designs of the later thirteenth century. The roofs were rebuilt, and the chancel extended to the east, lit by a fine four-light Decorated style window and two smaller flanking windows. In 1875-6 further work was carried out on the west front and the turret by the architect William Atkinson.
The liturgical arrangements and fittings of St Helen's, like the fabric, are an amalgam of elements of various dates. In the Middle Ages, there were altars to the Virgin, to St John the Baptist, and to St Michael. The finely-carved late medieval sculptures representing St Michael and God the Father and Christ receiving a soul re-used as label-stops either sides of the eastern arch of the north arcade perhaps derive from the chapel of St Michael. Apart from the font, the only other significant medieval fittings are the stained glass panels re-used in some of the south aisle windows and especially the early fourteenth-century glass in the west window (originally in the east window). This includes an image of St Helen, and a royal figure who could be the Emperor Constantine. As St Helen's was the church of the York glaziers, the stained glass in the church is an important reminder of the stained glass artists whose work has made York internationally famous.