Writing in 1863, William Grainge surmised that the buildings dated back to 1250. Muriel Swires, in a brief history of the church, found a documentary record dated 1320 when a chaplain was to be appointed "to celebrate mass every day in the chapel of the Blessed Virgin Mary, of Patheley Brigg, in Nidderdale, for the souls of William de Hamelton Aungier de Ripon and the aforesaid John and all the faithful departed." It is reasonable to suppose the church was built earlier, possibly on the site of an older one.
During the sixteenth century, the upper dale was a catholic stronghold at a time of recurrent persecution. In 1580-82 the High Commission launched an attack on those suspected of pursuing the 'old' religion - including Matthew Briggs, the curate of Pateley Bridge:
"Being thought and reported to be himself backwarde in matters of religion, and to seduce others by his synister Whisperinge in their eares, and being willed before the assemblie then and ther presente to yielde his opynion these two textes of scripture viz "Tu es Petrus" etc and "Hoc est corpus meum"....he shewed himselfe very unwillinge to do yt and at last spoke somethinge thereof verie absurdely, Wherof and for other causes the Commissioners movinge, the said Bryggs was committed to the Castell of Yorke....."
The first latin text, "Thou art Peter" and the second "This is my body" were the basis of Roman Catholic doctrine on papal authority and transubstantiation and were used to 'test' the beliefs of suspected Catholics.
The organisation and finance of the Church of England was not in a good state throughout the seventeenth century and many clergy were forced to live on small incomes. The curate of Pateley Bridge received nothing from the 'great' tithes corn, hay, wool and lamb, which were paid paid elsewhere. One source of difficulty was the practice of 'pluralism', of clergy holding several 'livings' and contracting out the work to poorly paid curates. To help remedy this, in 1704 Queen Anne created a fund of £16,000 to augment the stipends of lower paid clergy. A grant from the Queen's 'Bounty' increased the curate of Pateley Bridge's stipend from £20 to £26 3s 6d.
In 1738, the curate, James Pattison suffered a loss of income from the presence of an unlicensed 'strolling' clergyman, Francis Storey, who performed marriages in the area and pocketed the fee. In 1734, three couples were excommunicated for clandestine marriages by Storey. In the same year there were excommunications for 'ante-nuptial fornication' and 'Augustines Stoney for having two wives'.
Curate Pattison was opposed to the visits to Pateley of Thomas Lee, the harbinger of Methodism in the Dale. According to Lee, Pattison encouraged the mob which met him with blows and pelted him with mud and stones. However, matters improved and by 1780 the then curate, William Neeson, welcomed John Wesley to the town and gave him the use of the church.
In the following years however, the church fell into decay and closed in 1826, when it was too small for the congregation and too expensive to maintain. In addition the Vestry took advantage of government grants to subsidise new churches and St. Cuthbert's was opened in the same year.