On April 1, 1873, Rome appointed him coadjutor bishop of Msgr. Bourget, with later preferment. He received his episcopal ordination in the church of Gesù from Msgr. Alexandre Taschereau, Archbishop of Quebec.

He became the third bishop of Montreal on May 16, 1876 following the resignation of Msgr. Bourget. He was forty-nine years old. Ten years later, on June 8, 1886, Rome appointed him first Archbishop of Montreal with the bishops of Saint-Hyacinthe and Sherbrooke as suffragants.

Incidentally, it was under Msgr. Fabre that a third partition of the diocese was created in 1892 with the creation of the diocese of Valleyfield, in the southeast of the initial territory.

During the twenty years of his episcopate as titular bishop of Montreal, he had no auxiliary and presided at all the important celebrations. He ordained 210 priests from his diocese in addition to 820 other priests including 88 from other parts of Canada, America, or other dioceses; all of which were priests trained by the Grand Séminaire de Montréal. He confirmed 222,438 children and made 1,254 parish visits. His qualities as a liturgist and president of an assembly were greatly put to good use.

Like Msgr. Bourget, he welcomed ten religious communities from Europe to his diocese: The Little Sisters of the Poor, the Trappists, the Congregation of the Most Holy Redeemer, the Congregation of the Blessed Sacrament, the Franciscans, the Missionaries of the Company of Mary, the Marist Brothers, the Brothers of St Gabriel, the Brothers of the Sacred Heart, the Brothers of Christian Instruction.

A severe economic crisis during the last quarter of the 19th century, particularly between 1879 and 1884, forced Msgr. Fabre to face great financial difficulties in his diocese. High unemployment rates, strong urban population growth due to immigration, and the arrival of thousands of inhabitants in the city would destabilize the entire economy of Montreal. The Archdiocese first assumed the cumulative debt of $840,000 of the sixteen new parishes on the island of Montreal. Then, in his circular letter of June 10, 1879, Msgr. Fabre proposed some practical solutions. He asked each fabrique, as well as for religious communities and more affluent individuals, for an interest-free loan of $1,000. Bazaars were organised along with social evenings, collections, and donations. Msgr. Bourget, retired and sick, volunteered himself to search everywhere.

Nevertheless, Msgr. Fabre ensured that the Church of Montreal showed the greatest possible generosity to the unemployed and their families. With one of his priests, the popular priest Antoine Labelle, he promoted colonization.

With the economic situation having improved, construction began on the Saint-Jacques cathedra resumed in 1885 after having been interrupted for seven years. They were completed in 1894, 42 years after the fire in the previous cathedral built under Msgr. Bourget.

Let us also mention the steps taken by Msgr. Fabre to advance the cause of the Université de Montréal. The Congregation for the Evangelisation of Peoples, to which the Pontifical Charter of the University then belonged, had promised the institution status as a branch of Laval University. Thanks to the constitutional amendment of February 2, 1889 obtained from Rome by Msgr. Fabre, the Université de Montréal became quasi independent. Its new incorporation and the beginning of courses in the autumn of 1890 sanctioned the existence of the faculties of theology, law, medicine, and the arts.

Through his pastoral acts; visits, meetings, celebrations, as in his rigorous management and his social and cultural initiatives, Msgr. Fabre always showed himself to be an affable, jovial, conciliatory, and highly intelligent man. His kindness and popularity made him very comfortable in the presence of all manner of people. This did not, however, prevent him from raising his voice, sometimes with a certain rigorism, to condemn conduct or deviances that he considered harmful to his diocesan brothers.

He left his successor a healthy diocese with 450,000 faithful, 503 diocesan or religious priests, 33 male and female religious communities, and 164 parishes.

Msgr. Édouard-Charles Fabre died on December 30, 1896 in his episcopal residence at the age of 69, surrounded by the solicitude of his priests. At his request, there was no eulogy at his funeral. His mortal remains lie in the Cathedral, in the funeral chapel of the bishops.