Originally constructed of wood, it was replaced by a stone structure beginning in 1820 inspired (as were many churches of the day) by Saint Martin in the Fields in London.

The church enjoyed a papal visit from Pope John Paul II in September 1984; that year was the 200th anniversary of the precedent set by the laity of Halifax of forcing the repeal of the anti-Catholic legislation in Nova Scotia, and the British Empire.

In addition to being peppered by the glass shards, the paintings on the walls suffered water damage from a blizzard which entered the church through the broken windows.

In June 2019, work was begun to remove the layers of white paint (using scalpels) and restore damaged portions of the paintings—a project expected to continue until 2024.

[5] In 2024, Saint Mary's Cathedral Basilica welcomed the relic of the Blessed Carlo Acutis as part of the Archdiocese of Halifax-Yarmouth's Eucharistic congress.