A small building was erected for customs purposes in 1850 and in the following decades became increasingly inadequate as Brisbane emerged as the principal commercial centre and port of Queensland.

In March 1886 a design by Charles McLay was selected from many proposals in the Colonial Architect's Office for a new Brisbane Customs House.

The contract time was 30 months but because of difficulties with the supply of some materials, especially stone for the foundations, and alterations to the original plans, the building took longer than anticipated to complete and it was opened on 2 September 1889.

The copper-sheathed dome was constructed by sub-contracted coppersmith and brass founder, William Smith Henderson, of Perry Street, Petries' Bight.

A curved iron balustrade to the balconies included the royal cypher of the reigning sovereign, Queen Victoria, in the cast.

On 7 September 1889, a few days after the building was opened for business, the local Brisbane Courier newspaper drew attention to "the handsome and imposing appearance, especially as seen from the river or from Petrie's Bight" and predicted that the Brisbane Customs House with its tall columns, pilasters and large copper-sheathed dome would "become one of the features of the city".

Minor repairs were carried out throughout the 1890s, including some work in 1895 after 7 feet (2.1 m) of water inundated the basement during the 1893 Brisbane River floods.

[2] As a consequence of the Federation of Australia, the Brisbane Customs House, valued at £80,804 (£40,804 for the structure and £40,000 for the site), was transferred to the Australian Government by December 1908.

In 1947 major internal alterations were undertaken: all but two of the internal masonry walls were demolished; the timber floors were replaced by concrete slabs; the cedar staircase was removed and a new terrazzo one was installed at another location; mezzanine floors were erected in the Long Room; and the roof was replaced - without the original chimneys.

[2] Following the renovation, there is a restaurant and function centre within the building, and regular concerts and an art gallery occupies the lower floor.

[6] Protests erupted over concerns that the tower would be too close to the Customs House causing over-shadowing and the likely destruction of the fig tree.

[7] University of Queensland announced it would lodge a legal challenge against the approval of the project by Brisbane City Council, stating that the tower would be only 2.6 metres (8 ft 6 in) from the Customs House boundary, despite the council's own provisions in the City Plan 2014, which would require a 25 metres (82 ft) setback.

[11] The downstream end of the Brisbane central business district was selected to spur the development of wharves in the precinct known as Petrie Bight.

[4] Despite no government in the country having a coat of arms at the time, the building features a depiction on its facade of a shield between an emu and kangaroo.

The site is prominent due to the proximity to the river, the bend in Queen Street and the general topography which opens up many views to and from the building.

A prominent feature is the large copper dome at the semi-circular northern end which is a focal point viewed from both directions along Queen Street and from the river for ships arriving from Moreton Bay.

The architectural form of the building announces the northern edge of the city centre and is sympathetic to the landscape features of cliffs and river bends.

[2] Other features of the Brisbane Customs House which demonstrate its former use are more characteristic of late 19th century customs houses in Australia, especially the general design and planning arrangement of the building to include an imposing masonry facade, an impressive public space (the former Long Room now used for functions), a secure bonded warehouse (the former Queens Warehouse, now converted to an art gallery), offices and a secure boundary fence.

The Brisbane Customs House is a well proportioned and skilfully designed example of a Victorian building in the Renaissance mode executed to take best advantage of its dominant site and solve the practical problems of dual access from the town and from the river.

The 1890-91 Moggill sandstone retaining wall carries around the perimeter of the site reasonably intact and incorporates a wrought iron balustrade, masonry piers, stairs and rooms for the former underground privies at the river's edge.

The Brisbane Customs House has aesthetic value as a well proportioned and skilfully designed Victorian building in the Renaissance mode, executed to take best advantage of its dominant site and solve the practical problems of dual access from the town and from the river.