This Parish of St. John the Baptist was founded in 1699 in response to a petition drafted by the Anglican townsfolk of St. John's and sent to the Bishop of London, the Rt. Rev'd Henry Compton. In this petition, the people also requested help in the rebuilding of their church, which had been destroyed by fire in the course of hostilities with the French. The first rector was a former Royal Naval chaplain, the Rev'd John Jackson.
At least six wooden churches stood on or near this site. Those that survived the rigours of Newfoundland weather fell victim to accidental fires and military operations during the wars between the French and the British which finally resulted in British control of North America.
The first stone church was begun in 1843 under the direction of Aubrey Spencer, the first bishop of Newfoundland, but little progress was made on this relatively modest edifice beyond the laying of a cornerstone before Bishop Spencer resigned due to ill health.
The present Cathedral was begun in 1847 by Edward FeiId, the second bishop of NewfoundIand. Bishop Feild commissioned plans from the leading Gothic Revival architect George Gilbert Scott, who envisioned a more impressive cruciform structure with varied ornamentation in the twelfth-century English style. The Nave, built between 1847 and 1850, served as the entire Cathedral Church for 35 years until the Transepts, Chancel and Sanctuary were added in the period 1880-1885.
On July 8, 1892, the Cathedral was extensively damaged during the Great Fire. The roof timbers ignited, which caused the roof to collapse, bringing the clerestory walls and piers in the nave down with it. The intense heat caused the lead to melt in the glass windows, resulting in the complete destruction of all but two; the sole surviving stained-glass window can now be seen in the Sacristy. Restoration of the Cathedral commenced in 1893. By 1895, the Chancel and Transepts had been rebuilt, while the Nave reached completion in 1905.
The Anglican Cathedral of St. John the Baptist was designated a National Historic Site in 1981, and was designated a Registered Heritage Structure by the Heritage Foundation of Newfoundland and Labrador in 1991.