[1] The church had its beginnings when Bishop James Gillis, Vicar Apostolic of the Eastern District, invited the Society of Jesus to come to Edinburgh and set up a parish close to the city centre.

Initially, while the church was being built, Mass was celebrated in a temporary chapel on Hunter's Close in the Grassmarket part of the city.

From 1963 to 1990 there alterations made to make the church more compatible with the requirements of the post-Vatican II era, and the mural was covered over with wallpaper.

In addition, the parish worked with the nearby Little Sisters of the Poor care home in Gilmore Place until it closed in 2018.

[10] Speakers such as Michael L. Fitzgerald have been featured on topics such as Christian Muslim relations[11] and the centre has been awarded for its efforts to advance the ecological agenda through a series of talks and events.

[12][13] On 30 November 2020, St Andrew's Day, during the COVID-19 pandemic, it was officially renamed the Edinburgh Jesuit Centre and began hosting series of talks concerning contemporary issues and the Catholic Church.