[2] The original church was built using convict labour by orders of the colony's first chaplain, the Reverend Richard Johnson, in June 1793.

It was made from poor materials and gained a reputation as "the ugliest church in Christendom".

[8] During World War II the hall was used as a hostel for women officers, who were on leave in Sydney.

This was in partnership with the Church of England National Emergency Fund[9] On 1 November 2013 St Philip's merged with Holy Trinity Garrison Church in Millers Point to form a joint parish using both buildings for combined ministry.

[10] Prominent clergy in the life of the church include William Cowper, his son William Cowper (the first Australian-born cleric),[11] T. C. Hammond, Sydney James Kirkby and a former Archbishop of Sydney, Donald Robinson.