In 1860, Walsh was made rector of the Cathedral, but chose to resign the position in 1861 and resume his former place at St. Mary's, while from April 1862 he also served as Vicar General of the Archdiocese.

Having paid off the diocese's considerable debt, Walsh the undertook the construction of St. Peter's Cathedral, designed by Joseph Connolly[3] In August 1889 Bishop Walsh was appointed Archbishop of Toronto, and installed on 27 Nov 1889.

[5] Walsh also invited French Canadian clergy from Quebec to staff the French-speaking parishes in Kent and Essex counties.

In 1894, the Archbishop secured a $40,000 (the equivalent of $1.48 million in 2024) gift from Catholic railway magnate Hugh Ryan to build a three-storey surgical wing for St Michael's Hospital, Toronto.

[6][7] The expansion put the hospital on the path to becoming one of Canada's preeminent teaching University, with its state-of-the-art operating theatre designed to accommodate fifty medical students.