Many of the oldest inns in England have connections with monasteries and churches as rest houses. For instance, the Bingley Arms at Bardsey, known as the Priests' Inn, can trace its origins back to Saxon times in the 10th century. 

The Ship has a good deal of seasoned hard old timber.

The Ship may also have been a monastic or church rest house. It certainly goes back several centuries as an inn. It was almost certainly known as the Ship in the 17th century, because there is a token copper coin in existence, dated 1671, which shows a ship in full sale with the inscription "John Briggs in Aldborough his half penny". There was a John Briggs who occupied an acre of land in Aldborough at that time. Traders and landlords often issued small copper coins in the reign of Charles the Second when there was a shortage of small change. The antiquary, William Smith, writing in 1884, was of the opinion that the coin was of the Ship at Aldborough, close to the Ure rather than any of the other three or four Aldboroughs or Aldeburghs. The ship would then have had an acre or four roods of land.

The Ship may well have been the pub mentioned in the Aldborough parish records for 1596, when a man hired a gun from another man in a pub, gave him two pence to have a shot, crossed the road over to the church and took a shot over the minister as he was coming out of the pulpit. The shot missed. It seemed to be intended merely to put the fear of God into the minister, although the records do say that the paper where the gun was rammed came close to him as he was descending from the pulpit.

The name of the inn, as with the Ship at Milby, is an indication of the importance  of the river traffic downstream from Boroughbridge.

The Blackburn family ran the inn for more than 130 years: Thomas Blackburn in 1712, another Thomas Blackburn in 1747, his son Richard in the early 19th century and Ellen Blackburn as late as 1844.