The building was a proprietary chapel, the only one in the whole of Yorkshire, and one of only two Anglican churches to be dedicated to St Ninian in England.

A chapel of ease called St Ninian's was known to have been in existence on Baxtergate in Whitby since the late 14th century.

[10] Some of the original owners of the church included Thomas Fishburn and Thomas Milner; Fishburn's Yard in the town built three of the ships that Captain Cook used on his voyages, and Milner owned the Earl of Pembroke, which was bought by the Royal Navy and renamed Endeavour.

[13] As the structure is a proprietary chapel, the families of those who paid for the church inherit the ownership,[14] though by its closure, very few of the owners could be traced.

[30] In 1994, the Bishop of Whitby wrote to the Archbishop of York asking for the licence of St Ninian's to be revoked on account of the repairs needed to be made at the church.

[31][32] The original 30 investors in the church passed on their rights through inheritance, sale, transfer, and in at least one instance, bankruptcy.

[34] In 1998, the Archbishop of York (David Hope) revoked the licence for the church to hold traditional Anglican services after the dispute with the "traditionalist members could not be resolved".

[39] The cupboards in the vestry were fashioned to be like the locker's on ships, again a legacy of those who built the interior of the church in the first place.

[40] A Whitby mast-maker, Isaac Allanson, supplied the men and materials for the three galleries that line the church on three sides, with supports made from oak wood.

[44] The Architect Journal from 1874 described the building as a "debased edifice of Queen Anne, or any way, of Dolly Varden architecture..."[45] The chancel screen, polygonal timber pulpit, and stone font, all originate from the early 20th century.