It existed until 1835 when all offices and accounting departments of the Royal Navy were unified into the Department of the Accountant-General of the Navy.

The Navy Pay Office received money directly from HM Treasury.

The work of its staff was divided into a number of branches with specific areas of responsibility, these were overseen by the paymaster of the navy, the inspector of seamen's wills and the captains comptrolling payments of ships at Portsmouth, Plymouth and the Nore.

[3] The Navy Pay Office (domain of the Treasurer of the Navy and the Paymaster of the Navy) was independent of the Navy Board; though the board's commissioners were required to authorize payments, all funds transferred from HM Treasury were held and issued by the Navy Pay Office (which was also known as the Naval Treasury).

The Navy Pay Office consisted of a number of specific departments and offices that included:[4][5][6] Each branch within the Navy Pay Office was administered by a Chief Clerk each had a head cashier together with other supporting staff.