[4] At the suggestion of Bishop Benedict Joseph Fenwick, Fitzpatrick then enrolled at Petit Seminaire, run by the Sulpician Fathers, in Montreal, Quebec.

[6] After Fitzpatrick returned to Boston in November 1840, the diocese assigned him as a curate at Holy Cross Cathedral and St. Mary's Church in the North End.

[6] Fitzpatrick received his episcopal consecration on March 24, 1844, from Fenwick, with Bishops Richard Vincent Whelan and William Tyler serving as co-consecrators, at Georgetown.

[6] Fitzpatrick then assumed many of Fenwick's duties, including administering Confirmation, conducting episcopal visitations, investigating parish affairs, and preaching at the cathedral.

Following the outbreak of the Great Famine in Ireland Fitzpatrick strongly encouraged Catholics to contribute to the relief effort there.

On March 14, 1859, a staff member at a Boston public school whipped a Catholic boy for refusing to recite the Ten Commandments from a Protestant bible.

[2] During the Civil War (1861–1865), he supported President Abraham Lincoln and the Union, and made a special effort to provide Catholic chaplains for the Massachusetts regiments.

[2] He visited Belgium in 1862 for what he claimed as health reasons;[4] however, others (including Ambrose Dudley Mann and Henry Shelton Sanford) believed he was working for the Union cause in Europe.