The early history of the Trinity House has been lost, partly in the mists of time, but mostly in the loss of records surrendered during the Civil War. The house itself has been destroyed by fire on three occasions, the first in the Great Fire of London, 1666; then in 1714 when a fire destroyed the Custom House, most of Water Lane where the Trinity House was situated and a part of Tower Street; and again in 1940 when fire, caused by incendiary bombs, destroyed nearly all the possessions of the corporation, some of which they had owned for upwards of 300 years. Such early records as they possessed, however, and their plate, which were stored elsewhere, have survived.

The corporation received its first charter, a copy of which is in their possession, from King Henry VIII in 1514, and the probability is that a Guild or Fellowship of some sort had been in existence for some time before, possibly under the same name, as a hall and almshouses were standing in Deptford in that year.