In April 1889, Pearson's plans for the cathedral were approved for the original site bounded by George, Elizabeth and William Streets.It was a cruciform church with a wide nave, double aisles, apse and ambulatory, short transepts about halfway along the length of the building and an apsidal side chapel on the north.

The present Ann Street site was purchased in late 1899 because it was "central, commodious and had the natural advantage of being able to make the building erected on it a landmark for miles around".

[5] Frank Loughborough Pearson spent a year reworking his father's design and, on 22 May 1901, the Duke of Cornwall and York (later King George V) laid the foundation stone of the cathedral.

[4] The third stage of construction commenced in 1989 and was completed in 2009 (with the exception of 29 life-sized statues on the west front and a set of cloisters on the north side of the cathedral which have yet to be commissioned).

This stage of work was overseen by Peter Dare, Master Mason of Exeter Cathedral in England and carried out by stonemasons from Wagners.

[15] The third stage of construction cost A$40 million which was raised by public donations, bequests and grants from the federal, state and local governments.

[citation needed] The copper-clad western spires were lifted into position on 1 March 2008 and subsequently blessed by Bishop John Parkes.

[citation needed] In 2009 as part of the Q150 celebrations, St John's Cathedral was announced as one of the Q150 Icons of Queensland for its role as a "structure and engineering feat".

[16] The Archbishop of Brisbane, Phillip Aspinall, officially reconsecrated the completed cathedral on 29 October 2009, attended by about 1,500 people, 108 years after the laying of the foundation stone.

The cathedral's eastern wall had also bowed approximately 2.5 mm from the force of the wind, leaving it in danger of structural failure.

[19] In 2015, a series of statues carved by Rhyl Hinwood, costing $45,000 each, were purchased and blessed by Archbishop Aspinall before being installed on the cathedral's facade.

[20] On 20 September 2022, St John's Cathedral held a service of thanksgiving marking the reign of Elizabeth II, Queen of Australia.

The cathedral was designed in the Gothic revival style by John Loughborough Pearson, one of England's leading church architects of the late 19th century and bears similarities to Truro Cathedral in Cornwall, also designed by Pearson, although the architecture of St John's is more decidedly French Gothic in inspiration.

[10] The granite and basalt used in the foundations and at the base of the columns came from Harcourt and Footscray in Victoria and the sandstone for the window dressings, doorways and arcading came from Pyrmont, New South Wales.

[21] The initial architectural impact is achieved via its lofty ceilings, tall and delicately proportioned columns and low level lighting.

[23] The north and south aisles, representing a bird's folded wings, are separated from the nave, or body, by Pearson's slender piers.

This can be seen in St John's in the atmosphere of the building created by the mass of stone pillars, ceilings and arches, the quality of the sandstone and the basic simplicity of the design and, apart from the west front, minimal ornamentation.

In front of the altar in the sanctuary floor are two pieces of mosaic from the Holy Land, brought back after being uncovered during the First World War by the Australian Light Horse Regiment.

The other is a fragment from the floor of a 6th-century Christian church at Gaza and is part of a larger mosaic now housed in the Australian War Memorial in Canberra.

[12] Beyond the high altar the cathedral ends in a semicircular apse and ambulatory (processional aisle), a link to the architecture's French-Norman past.

These buildings provide the traditional experience of only having a full view of the cathedral when quite close (after having wound one's way through narrow medieval city streets) thus adding to the impact and feeling of grandeur.

St Martin's shows similarities to the "Red Brick House" designed by Philip Webb for William Morris.